OR2T10

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

Basic information

Region (hg38): 1:248590487-248597700

Links

ENSG00000184022 ∙ NCBI:127069 ∙ ∙ HGNC:19573 ∙ Uniprot:Q8NGZ9 ∙ 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 OR2T10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2T10 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			9	2		11
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	2	0

Variants in OR2T10

This is a list of pathogenic ClinVar variants found in the OR2T10 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-248592840-G-A		not specified	Uncertain significance (Jan 03, 2022)
1-248592850-C-T		not specified	Likely benign (Jun 07, 2024)
1-248592950-C-A		not specified	Uncertain significance (Aug 08, 2023)
1-248593077-A-G		not specified	Likely benign (Jul 08, 2022)
1-248593155-A-G		not specified	Uncertain significance (May 07, 2024)
1-248593282-C-T		not specified	Likely benign (Sep 26, 2023)
1-248593287-G-C		not specified	Uncertain significance (Apr 15, 2024)
1-248593296-A-G		not specified	Uncertain significance (Jun 12, 2023)
1-248593387-G-A		not specified	Uncertain significance (Jul 09, 2021)
1-248593420-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-248593570-A-G		not specified	Uncertain significance (Jan 17, 2023)
1-248593698-G-A		not specified	Uncertain significance (Feb 26, 2024)
1-248593699-G-A		not specified	Uncertain significance (Jul 11, 2023)
1-248593738-C-T		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2T10	protein_coding	protein_coding	ENST00000330500	1	1049

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000656	0.310	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.297	161	172	0.936	0.00000840	2040
Missense in Polyphen		39	43.432	0.89795		604
Synonymous	1.57	48	63.9	0.751	0.00000303	622
Loss of Function	-0.721	4	2.72	1.47	1.13e-7	37

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: 0.0990

Intolerance Scores

• loftool: 0.885
• rvis_EVS: 1.68
• rvis_percentile_EVS: 96.36

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0632

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