OR9Q1

olfactory receptor family 9 subfamily Q member 1, the group of Olfactory receptors, family 9

Basic information

Region (hg38): 11:58023880-58181616

Links

ENSG00000186509 ∙ NCBI:219956 ∙ ∙ HGNC:14724 ∙ Uniprot:Q8NGQ5 ∙ 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 OR9Q1 gene.

• Inborn genetic diseases (37 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR9Q1 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			25	2		27
Total	0	0	36	2	0

Variants in OR9Q1

This is a list of pathogenic ClinVar variants found in the OR9Q1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-58030960-C-T		not specified	Uncertain significance (Nov 03, 2023)
11-58031001-A-T		not specified	Uncertain significance (Oct 06, 2022)
11-58031058-A-G		not specified	Uncertain significance (Aug 08, 2022)
11-58031069-C-A		not specified	Uncertain significance (Jan 04, 2022)
11-58031124-C-T		not specified	Likely benign (Sep 01, 2021)
11-58031125-G-A		not specified	Uncertain significance (Sep 07, 2022)
11-58031169-A-G		not specified	Uncertain significance (Jul 20, 2021)
11-58031209-G-T		not specified	Uncertain significance (Sep 17, 2021)
11-58031220-G-T		not specified	Uncertain significance (Nov 28, 2023)
11-58031289-G-A		not specified	Uncertain significance (Sep 30, 2021)
11-58031316-A-G		not specified	Uncertain significance (Aug 12, 2022)
11-58031472-G-A		not specified	Uncertain significance (Oct 14, 2023)
11-58031527-C-T		not specified	Uncertain significance (Mar 11, 2024)
11-58031628-G-A		not specified	Uncertain significance (Dec 21, 2022)
11-58031722-G-T		not specified	Uncertain significance (Jun 26, 2023)
11-58031771-C-A		not specified	Uncertain significance (Feb 26, 2024)
11-58031781-G-A		not specified	Uncertain significance (Aug 26, 2022)
11-58031805-G-A		not specified	Uncertain significance (Dec 02, 2022)
11-58031867-G-T			Likely benign (Apr 01, 2022)
11-58031898-G-C		not specified	Uncertain significance (Aug 30, 2022)
11-58118547-C-T		not specified	Uncertain significance (Jul 09, 2021)
11-58118556-C-T		not specified	Uncertain significance (Feb 15, 2023)
11-58118561-T-C		not specified	Uncertain significance (Apr 19, 2023)
11-58118625-C-T		not specified	Uncertain significance (Oct 20, 2023)
11-58118634-C-T		not specified	Uncertain significance (Apr 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR9Q1	protein_coding	protein_coding	ENST00000335397	1	157736

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000839	0.570	125683	0	41	125724	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.221	181	173	1.05	0.00000902	2016
Missense in Polyphen		52	56.258	0.92432		752
Synonymous	0.00948	70	70.1	0.999	0.00000380	651
Loss of Function	0.434	5	6.16	0.811	2.55e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000850	0.000850
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000969	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

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: 0.0818

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.88

Haploinsufficiency Scores

• pHI: 0.0487
• hipred: N
• hipred_score: 0.131

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0696

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr1500

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;sensory perception of smell;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;odorant binding