OR6K2

olfactory receptor family 6 subfamily K member 2, the group of Olfactory receptors, family 6

Basic information

Region (hg38): 1:158699678-158700652

Links

ENSG00000196171 ∙ NCBI:81448 ∙ ∙ HGNC:15029 ∙ Uniprot:Q8NGY2 ∙ 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 OR6K2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR6K2 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			30	2		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	0

Variants in OR6K2

This is a list of pathogenic ClinVar variants found in the OR6K2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-158699688-T-C		not specified	Uncertain significance (Oct 12, 2022)
1-158699694-G-A		not specified	Uncertain significance (Jan 22, 2024)
1-158699697-G-A		not specified	Uncertain significance (Jul 14, 2023)
1-158699701-C-G		not specified	Uncertain significance (Jun 12, 2023)
1-158699704-G-C		not specified	Uncertain significance (Nov 17, 2023)
1-158699706-C-A		Malignant tumor of prostate	Uncertain significance (-)
1-158699748-A-G		not specified	Uncertain significance (Aug 30, 2021)
1-158699787-A-G		not specified	Uncertain significance (Feb 14, 2023)
1-158699791-G-A		not specified	Uncertain significance (Feb 17, 2023)
1-158699800-A-T		not specified	Uncertain significance (Oct 13, 2021)
1-158699820-G-T		not specified	Uncertain significance (Nov 01, 2022)
1-158699874-T-G		not specified	Uncertain significance (Jul 19, 2022)
1-158699877-A-G		not specified	Uncertain significance (Feb 21, 2024)
1-158699950-G-A		not specified	Uncertain significance (Apr 23, 2024)
1-158699979-A-G		not specified	Uncertain significance (Jun 18, 2021)
1-158699983-C-CT			not provided (-)
1-158699994-T-A		not specified	Likely benign (Jan 19, 2022)
1-158699997-T-C		not specified	Uncertain significance (May 24, 2024)
1-158700045-A-T		not specified	Uncertain significance (Dec 19, 2022)
1-158700057-A-G		not specified	Uncertain significance (Aug 16, 2022)
1-158700065-C-T		not specified	Uncertain significance (Jun 22, 2023)
1-158700078-C-A		not specified	Uncertain significance (Dec 14, 2023)
1-158700088-T-C		not specified	Uncertain significance (Jan 31, 2023)
1-158700174-G-A		not specified	Likely benign (Jun 07, 2024)
1-158700189-G-A		not specified	Uncertain significance (Sep 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR6K2	protein_coding	protein_coding	ENST00000359610	1	1118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.42e-7	0.0876	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.24	227	180	1.26	0.00000940	2129
Missense in Polyphen		61	52.89	1.1533		715
Synonymous	-0.437	71	66.5	1.07	0.00000357	672
Loss of Function	-0.697	9	7.01	1.28	4.62e-7	71

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: 0.939
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.46

Haploinsufficiency Scores

• pHI: 0.0655
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0159

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr420

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