OR9A4

olfactory receptor family 9 subfamily A member 4, the group of Olfactory receptors, family 9

Basic information

Region (hg38): 7:141916398-141920625

Links

ENSG00000258083 ∙ NCBI:130075 ∙ ∙ HGNC:15095 ∙ Uniprot:Q8NGU2 ∙ 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 OR9A4 gene.

• Inborn genetic diseases (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR9A4 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			12			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	12	0	0

Variants in OR9A4

This is a list of pathogenic ClinVar variants found in the OR9A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-141919044-C-G		not specified	Uncertain significance (Jan 03, 2024)
7-141919062-G-A		not specified	Uncertain significance (Jan 10, 2023)
7-141919151-A-G		not specified	Uncertain significance (Sep 20, 2023)
7-141919153-A-G		not specified	Uncertain significance (Feb 15, 2023)
7-141919153-A-T		not specified	Uncertain significance (Feb 28, 2024)
7-141919204-C-T		not specified	Uncertain significance (Jun 13, 2023)
7-141919248-G-A		not specified	Uncertain significance (Feb 23, 2023)
7-141919327-T-C		not specified	Uncertain significance (Dec 22, 2023)
7-141919417-G-C		not specified	Uncertain significance (Apr 27, 2023)
7-141919474-T-A		not specified	Uncertain significance (Feb 13, 2024)
7-141919488-T-C		not specified	Uncertain significance (Apr 04, 2023)
7-141919548-A-G		not specified	Uncertain significance (Dec 02, 2021)
7-141919575-C-G		not specified	Uncertain significance (Nov 14, 2023)
7-141919602-T-C		not specified	Uncertain significance (Nov 18, 2022)
7-141919602-T-G		not specified	Uncertain significance (Jul 16, 2021)
7-141919663-A-G		not specified	Uncertain significance (Dec 21, 2023)
7-141919764-G-A		not specified	Uncertain significance (Feb 16, 2023)
7-141919795-G-T		not specified	Uncertain significance (Aug 02, 2021)
7-141919814-G-C		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR9A4	protein_coding	protein_coding	ENST00000548136	1	1093

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.18e-7	0.0583	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.746	199	171	1.16	0.00000978	2058
Missense in Polyphen		56	50.572	1.1073		716
Synonymous	-0.964	75	65.1	1.15	0.00000363	640
Loss of Function	-1.05	9	6.19	1.45	3.54e-7	82

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: 0.741
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.131

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.192

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr460

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