OR2T2

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

Basic information

Region (hg38): 1:248445511-248455725

Previous symbols: [ "OR2T2P" ]

Links

ENSG00000196240 ∙ NCBI:401992 ∙ ∙ HGNC:14725 ∙ Uniprot:Q6IF00 ∙ 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 OR2T2 gene.

• Inborn genetic diseases (10 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2T2 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				4		4
missense			9	1	2	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	5	2

Variants in OR2T2

This is a list of pathogenic ClinVar variants found in the OR2T2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-248452837-G-A		not specified	Likely benign (Apr 25, 2023)
1-248452898-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-248453036-C-T		not specified	Uncertain significance (Dec 22, 2023)
1-248453100-G-A			Likely benign (Aug 02, 2017)
1-248453107-C-T			Benign (Aug 02, 2017)
1-248453117-C-A			Benign (Aug 02, 2017)
1-248453191-C-T		not specified	Uncertain significance (Apr 06, 2022)
1-248453213-G-A		not specified	Uncertain significance (Dec 16, 2023)
1-248453312-C-T		not specified	Uncertain significance (Sep 27, 2021)
1-248453315-G-A		not specified	Uncertain significance (Jun 07, 2022)
1-248453350-G-A		not specified	Uncertain significance (Jan 16, 2024)
1-248453367-C-T			Likely benign (Jan 01, 2023)
1-248453410-G-A		not specified	Uncertain significance (Sep 25, 2023)
1-248453440-A-G		not specified	Uncertain significance (Sep 13, 2023)
1-248453501-G-A		not specified	Uncertain significance (Jan 03, 2022)
1-248453503-C-T		not specified	Uncertain significance (Jul 26, 2022)
1-248453529-C-T			Likely benign (Mar 01, 2020)
1-248453556-C-T			Likely benign (Aug 01, 2022)
1-248453620-G-A		not specified	Uncertain significance (Mar 29, 2023)
1-248453685-A-T		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2T2	protein_coding	protein_coding	ENST00000342927	1	1054

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.205	0.659	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.32	218	170	1.28	0.00000895	1994
Missense in Polyphen		89	60.572	1.4693		763
Synonymous	-1.26	82	68.7	1.19	0.00000389	640
Loss of Function	1.01	1	2.84	0.353	1.18e-7	42

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: 0.103

Intolerance Scores

• loftool: 0.934
• rvis_EVS: 1
• rvis_percentile_EVS: 90.62

Haploinsufficiency Scores

• pHI: 0.217
• hipred: N
• hipred_score: 0.318

Essentials

• 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

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