OR9K2

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

Basic information

Region (hg38): 12:55126406-55132750

Links

ENSG00000170605 ∙ NCBI:441639 ∙ ∙ HGNC:15339 ∙ Uniprot:Q8NGE7 ∙ 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 OR9K2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR9K2 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	21	0	0

Variants in OR9K2

This is a list of pathogenic ClinVar variants found in the OR9K2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-55129833-C-A		not specified	Uncertain significance (Oct 29, 2021)
12-55129851-C-G		not specified	Uncertain significance (Dec 27, 2023)
12-55129897-G-C		not specified	Uncertain significance (Jun 03, 2024)
12-55130003-C-T		not specified	Uncertain significance (Jan 26, 2023)
12-55130018-A-G		not specified	Uncertain significance (Oct 12, 2022)
12-55130033-G-A		not specified	Uncertain significance (Mar 25, 2024)
12-55130039-C-A		not specified	Uncertain significance (May 09, 2024)
12-55130075-G-A		not specified	Uncertain significance (Feb 15, 2023)
12-55130117-A-G		not specified	Uncertain significance (Sep 27, 2022)
12-55130125-T-G		not specified	Uncertain significance (May 31, 2023)
12-55130127-C-T		not specified	Uncertain significance (Nov 09, 2021)
12-55130190-C-T		not specified	Uncertain significance (Sep 14, 2022)
12-55130204-G-A		not specified	Uncertain significance (Dec 06, 2022)
12-55130206-C-A		not specified	Uncertain significance (Oct 30, 2023)
12-55130228-C-A		not specified	Uncertain significance (Oct 20, 2023)
12-55130232-T-C		not specified	Uncertain significance (Mar 19, 2024)
12-55130286-C-T		not specified	Uncertain significance (Aug 16, 2021)
12-55130387-C-T		not specified	Uncertain significance (Sep 27, 2021)
12-55130405-T-A		not specified	Uncertain significance (Feb 16, 2023)
12-55130436-T-C		not specified	Uncertain significance (Jan 05, 2022)
12-55130499-T-C		not specified	Uncertain significance (Aug 22, 2023)
12-55130524-G-T		not specified	Uncertain significance (Sep 16, 2021)
12-55130589-G-A		not specified	Uncertain significance (Aug 08, 2022)
12-55130603-G-A		not specified	Uncertain significance (Jun 02, 2023)
12-55130672-T-G		not specified	Uncertain significance (Mar 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR9K2	protein_coding	protein_coding	ENST00000305377	1	1122

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.37e-7	0.0732	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.31	225	176	1.28	0.00000863	2195
Missense in Polyphen		58	39.33	1.4747		562
Synonymous	-0.800	71	62.9	1.13	0.00000293	695
Loss of Function	-1.13	8	5.21	1.54	2.19e-7	89

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: 0.878
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.17

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0315

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr826

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