OR6K3

olfactory receptor family 6 subfamily K member 3, the group of Olfactory receptors, family 6

Basic information

Region (hg38): 1:158716326-158720720

Links

ENSG00000203757 ∙ NCBI:391114 ∙ ∙ HGNC:15030 ∙ Uniprot:Q8NGY3 ∙ 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 OR6K3 gene.

• Inborn genetic diseases (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR6K3 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in OR6K3

This is a list of pathogenic ClinVar variants found in the OR6K3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-158717179-G-T		not specified	Uncertain significance (Aug 08, 2022)
1-158717206-A-G		not specified	Uncertain significance (Aug 08, 2022)
1-158717220-G-A		not specified	Uncertain significance (Jan 09, 2024)
1-158717247-C-T		not specified	Uncertain significance (Dec 19, 2023)
1-158717319-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-158717322-T-A		not specified	Uncertain significance (Jul 14, 2021)
1-158717338-G-A		not specified	Uncertain significance (Feb 13, 2024)
1-158717346-A-C		not specified	Uncertain significance (Feb 28, 2024)
1-158717362-C-T		not specified	Uncertain significance (Dec 19, 2022)
1-158717391-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-158717401-T-G		not specified	Uncertain significance (Feb 12, 2024)
1-158717500-T-C		not specified	Uncertain significance (Feb 05, 2024)
1-158717521-C-T		not specified	Uncertain significance (Nov 22, 2023)
1-158717541-G-A		not specified	Uncertain significance (Sep 19, 2023)
1-158717582-G-T		not specified	Uncertain significance (Aug 08, 2022)
1-158717662-C-T		not specified	Uncertain significance (Jun 18, 2021)
1-158717671-A-G		not specified	Uncertain significance (Dec 07, 2023)
1-158717700-C-T		not specified	Uncertain significance (Jul 20, 2021)
1-158717701-G-A		not specified	Uncertain significance (Feb 05, 2024)
1-158717714-C-T		not specified	Uncertain significance (Jun 01, 2023)
1-158717721-T-C		not specified	Uncertain significance (Mar 29, 2022)
1-158717724-C-T		not specified	Uncertain significance (Dec 13, 2022)
1-158717923-T-A		not specified	Likely benign (Feb 01, 2023)
1-158717962-C-A		not specified	Uncertain significance (Dec 21, 2022)
1-158717962-C-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR6K3	protein_coding	protein_coding	ENST00000368145	1	996

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0929	0.587	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.419	183	168	1.09	0.00000823	2082
Missense in Polyphen		65	50.152	1.2961		723
Synonymous	-1.43	77	62.6	1.23	0.00000325	630
Loss of Function	0.0285	1	1.03	0.970	4.33e-8	13

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: 0.0968

Intolerance Scores

• loftool: 0.614
• rvis_EVS: 1.02
• rvis_percentile_EVS: 90.98

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.171

Gene Damage Prediction

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

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