OR9A2

olfactory receptor family 9 subfamily A member 2, the group of Olfactory receptors, family 9

Basic information

Region (hg38): 7:143026200-143027132

Links

ENSG00000179468 ∙ NCBI:135924 ∙ ∙ HGNC:15093 ∙ Uniprot:Q8NGT5 ∙ 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 OR9A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR9A2 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			21	3		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	21	3	0

Variants in OR9A2

This is a list of pathogenic ClinVar variants found in the OR9A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-143026225-C-T		not specified	Uncertain significance (Feb 28, 2023)
7-143026246-G-T		not specified	Uncertain significance (Dec 01, 2024)
7-143026260-G-T		not specified	Uncertain significance (Jul 14, 2024)
7-143026273-G-C		not specified	Uncertain significance (Feb 15, 2023)
7-143026288-T-A		not specified	Uncertain significance (Jul 30, 2024)
7-143026307-C-T		not specified	Uncertain significance (Mar 28, 2024)
7-143026342-A-G		not specified	Likely benign (Feb 02, 2024)
7-143026385-T-A		not specified	Uncertain significance (Jul 14, 2021)
7-143026400-C-A		not specified	Uncertain significance (Aug 12, 2021)
7-143026418-A-G		not specified	Uncertain significance (Dec 07, 2023)
7-143026421-C-T		not specified	Uncertain significance (May 27, 2022)
7-143026444-C-T		not specified	Uncertain significance (Oct 26, 2021)
7-143026459-G-A		not specified	Uncertain significance (Aug 02, 2023)
7-143026541-T-C		not specified	Uncertain significance (Jan 08, 2024)
7-143026588-T-A		not specified	Uncertain significance (Jan 24, 2024)
7-143026672-C-A		not specified	Uncertain significance (Jul 16, 2024)
7-143026676-T-C		not specified	Uncertain significance (Dec 07, 2021)
7-143026723-C-T		not specified	Uncertain significance (Jul 09, 2024)
7-143026726-G-A		not specified	Uncertain significance (Jul 31, 2024)
7-143026726-G-T		not specified	Uncertain significance (Mar 30, 2024)
7-143026759-G-C		not specified	Uncertain significance (Mar 19, 2024)
7-143026784-C-T		not specified	Uncertain significance (Nov 18, 2022)
7-143026792-A-G		not specified	Uncertain significance (Jun 12, 2023)
7-143026829-A-C		not specified	Uncertain significance (Oct 19, 2024)
7-143026858-T-C		not specified	Likely benign (Jun 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR9A2	protein_coding	protein_coding	ENST00000350513	1	1038

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000289	0.580	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.523	150	169	0.887	0.00000854	2028
Missense in Polyphen		54	52.086	1.0368		707
Synonymous	0.641	60	66.7	0.900	0.00000337	636
Loss of Function	0.559	6	7.67	0.782	4.08e-7	96

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: 0.0950

Intolerance Scores

• loftool: 0.825
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.65

Haploinsufficiency Scores

• pHI: 0.0928
• hipred: N
• hipred_score: 0.131
• ghis: 0.394

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0786

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr459

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