OR2T6

olfactory receptor family 2 subfamily T member 6, the group of Olfactory receptors, family 2

Basic information

Region (hg38): 1:248375746-248391811

Previous symbols: [ "OR2T6P", "OR2T9" ]

Links

ENSG00000198104 ∙ NCBI:254879 ∙ ∙ HGNC:15018 ∙ Uniprot:Q8NHC8 ∙ 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 OR2T6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2T6 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			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	0

Variants in OR2T6

This is a list of pathogenic ClinVar variants found in the OR2T6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-248387668-C-G		not specified	Uncertain significance (Dec 30, 2023)
1-248387670-A-G		not specified	Uncertain significance (Jul 13, 2021)
1-248387741-A-G		not specified	Uncertain significance (Mar 15, 2024)
1-248387819-A-C		not specified	Uncertain significance (Feb 01, 2023)
1-248387877-G-C		not specified	Uncertain significance (May 24, 2023)
1-248387882-A-G		not specified	Uncertain significance (Aug 16, 2022)
1-248387978-G-A		not specified	Uncertain significance (Nov 21, 2023)
1-248388000-G-A		not specified	Likely benign (Aug 02, 2023)
1-248388008-G-A		not specified	Uncertain significance (Apr 13, 2022)
1-248388059-G-A		not specified	Uncertain significance (Mar 31, 2024)
1-248388060-G-A		not specified	Uncertain significance (May 02, 2024)
1-248388075-G-A		not specified	Uncertain significance (Sep 07, 2022)
1-248388087-C-T		not specified	Uncertain significance (Oct 03, 2022)
1-248388108-C-T		not specified	Uncertain significance (Apr 16, 2024)
1-248388200-G-T		not specified	Uncertain significance (Dec 19, 2022)
1-248388271-T-G		not specified	Uncertain significance (Oct 27, 2022)
1-248388272-C-G		not specified	Uncertain significance (Jul 05, 2023)
1-248388339-A-T		not specified	Uncertain significance (Jul 20, 2021)
1-248388345-T-C		not specified	Likely benign (Nov 15, 2021)
1-248388384-A-G		not specified	Uncertain significance (Oct 14, 2023)
1-248388408-C-A		not specified	Uncertain significance (Mar 20, 2023)
1-248388492-G-A		not specified	Uncertain significance (Jun 24, 2022)
1-248388500-A-C		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2T6	protein_coding	protein_coding	ENST00000355728	1	927

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000414	0.236	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.448	194	177	1.09	0.00000894	2027
Missense in Polyphen		56	55.081	1.0167		735
Synonymous	-1.53	88	71.5	1.23	0.00000408	608
Loss of Function	-0.469	6	4.88	1.23	2.04e-7	67

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: 0.0951

Intolerance Scores

• loftool: 0.555
• rvis_EVS: 2.46
• rvis_percentile_EVS: 98.59

Haploinsufficiency Scores

• pHI: 0.0532
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0437

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr720

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