OR52K1

olfactory receptor family 52 subfamily K member 1, the group of Olfactory receptors, family 52

Basic information

Region (hg38): 11:4482646-4493497

Links

ENSG00000196778 ∙ NCBI:390036 ∙ ∙ HGNC:15222 ∙ Uniprot:Q8NGK4 ∙ 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 OR52K1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR52K1 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				1		1
missense			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in OR52K1

This is a list of pathogenic ClinVar variants found in the OR52K1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-4488916-A-G		not specified	Uncertain significance (Jan 16, 2024)
11-4488949-G-A		not specified	Uncertain significance (Feb 28, 2024)
11-4488956-T-G		not specified	Uncertain significance (Nov 16, 2021)
11-4489042-C-T		not specified	Uncertain significance (Nov 14, 2023)
11-4489046-T-C		not specified	Uncertain significance (Mar 29, 2022)
11-4489061-A-G		not specified	Uncertain significance (Aug 02, 2021)
11-4489114-G-A		not specified	Uncertain significance (Jan 29, 2024)
11-4489124-T-C		not specified	Uncertain significance (Jun 10, 2022)
11-4489127-C-A		not specified	Uncertain significance (Jun 06, 2023)
11-4489145-A-G		not specified	Uncertain significance (Feb 10, 2023)
11-4489168-A-G		not specified	Uncertain significance (Oct 20, 2023)
11-4489188-C-G		not specified	Uncertain significance (May 02, 2024)
11-4489189-T-C		not specified	Uncertain significance (Feb 28, 2023)
11-4489298-A-T		not specified	Uncertain significance (Jun 16, 2024)
11-4489304-C-T		not specified	Uncertain significance (Jul 05, 2023)
11-4489323-C-T			Likely benign (Sep 01, 2022)
11-4489411-T-G		not specified	Uncertain significance (Oct 17, 2023)
11-4489415-G-T		not specified	Uncertain significance (Mar 20, 2024)
11-4489444-G-C		not specified	Uncertain significance (May 02, 2024)
11-4489600-G-A		not specified	Uncertain significance (Jul 20, 2021)
11-4489639-A-G		not specified	Uncertain significance (Feb 21, 2024)
11-4489648-A-G		not specified	Uncertain significance (Apr 15, 2024)
11-4489663-A-C		not specified	Uncertain significance (Jun 06, 2023)
11-4489664-C-G		not specified	Uncertain significance (May 03, 2023)
11-4489684-G-A		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR52K1	protein_coding	protein_coding	ENST00000307632	1	1030

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.93e-8	0.0203	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.35	225	175	1.29	0.00000943	2040
Missense in Polyphen		60	47.972	1.2507		669
Synonymous	-5.45	122	65.8	1.86	0.00000326	679
Loss of Function	-2.20	9	4.16	2.17	1.79e-7	64

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: 0.0866

Intolerance Scores

• loftool: 0.824
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.2

Haploinsufficiency Scores

• pHI: 0.0786
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

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