OR10T2

olfactory receptor family 10 subfamily T member 2, the group of Olfactory receptors, family 10

Basic information

Region (hg38): 1:158398522-158399466

Links

ENSG00000186306 ∙ NCBI:128360 ∙ ∙ HGNC:14816 ∙ Uniprot:Q8NGX3 ∙ 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 OR10T2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR10T2 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			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	0

Variants in OR10T2

This is a list of pathogenic ClinVar variants found in the OR10T2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-158398586-T-C		not specified	Uncertain significance (Jun 07, 2024)
1-158398617-A-T		not specified	Uncertain significance (Feb 23, 2023)
1-158398667-G-A		not specified	Uncertain significance (Mar 25, 2024)
1-158398668-C-A		not specified	Uncertain significance (Mar 25, 2024)
1-158398703-G-A		not specified	Uncertain significance (Aug 21, 2023)
1-158398704-C-A		not specified	Uncertain significance (Aug 21, 2023)
1-158398733-A-C		not specified	Uncertain significance (Feb 23, 2023)
1-158398883-A-G		not specified	Uncertain significance (Jul 06, 2021)
1-158398971-C-G		not specified	Uncertain significance (Jun 09, 2022)
1-158398988-G-A		not specified	Uncertain significance (May 18, 2023)
1-158399043-C-G		not specified	Uncertain significance (Feb 22, 2023)
1-158399105-T-C		not specified	Uncertain significance (Jun 28, 2023)
1-158399118-C-A		not specified	Uncertain significance (Jul 05, 2023)
1-158399127-G-A		not specified	Likely benign (Dec 20, 2021)
1-158399135-G-A		not specified	Uncertain significance (Apr 24, 2024)
1-158399148-C-A		not specified	Uncertain significance (Dec 19, 2023)
1-158399172-C-T		not specified	Uncertain significance (Apr 28, 2022)
1-158399180-A-G		not specified	Uncertain significance (Nov 21, 2022)
1-158399180-A-T		not specified	Uncertain significance (Apr 26, 2023)
1-158399233-G-C		not specified	Uncertain significance (Oct 13, 2023)
1-158399250-A-G		not specified	Uncertain significance (Dec 07, 2021)
1-158399285-T-C		not specified	Uncertain significance (Jul 05, 2023)
1-158399287-C-T		not specified	Uncertain significance (Aug 02, 2022)
1-158399313-A-G		not specified	Uncertain significance (May 16, 2022)
1-158399330-A-G		not specified	Uncertain significance (Sep 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR10T2	protein_coding	protein_coding	ENST00000334438	1	945

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.120	0.788	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.811	194	165	1.18	0.00000772	2019
Missense in Polyphen		53	55.154	0.96095		750
Synonymous	-1.46	79	64.2	1.23	0.00000285	676
Loss of Function	1.34	2	5.34	0.375	2.99e-7	80

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: 0.676
• rvis_EVS: 2.07
• rvis_percentile_EVS: 97.79

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.159

Gene Damage Prediction

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

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