OR52N5

olfactory receptor family 52 subfamily N member 5, the group of Olfactory receptors, family 52

Basic information

Region (hg38): 11:5776165-5783355

Links

ENSG00000181009 ∙ NCBI:390075 ∙ ∙ HGNC:15231 ∙ Uniprot:Q8NH56 ∙ 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 OR52N5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR52N5 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			14	3		17
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	4	0

Variants in OR52N5

This is a list of pathogenic ClinVar variants found in the OR52N5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-5777706-C-T		not specified	Uncertain significance (Apr 26, 2023)
11-5777730-T-C		not specified	Uncertain significance (Oct 02, 2023)
11-5777752-G-T		not specified	Uncertain significance (May 13, 2024)
11-5777783-G-C		not specified	Uncertain significance (Nov 03, 2022)
11-5777785-T-C		not specified	Likely benign (Dec 16, 2023)
11-5777851-C-A		not specified	Uncertain significance (Jul 14, 2021)
11-5777863-T-C		not specified	Uncertain significance (May 17, 2023)
11-5777934-G-A		not specified	Likely benign (Dec 20, 2021)
11-5777974-A-C		not specified	Uncertain significance (Oct 03, 2022)
11-5777997-A-C		not specified	Uncertain significance (May 09, 2023)
11-5778134-AGG-A			Likely benign (Dec 01, 2022)
11-5778294-T-C		not specified	Uncertain significance (May 14, 2024)
11-5778369-T-C		not specified	Uncertain significance (Jun 28, 2023)
11-5778412-G-A		not specified	Uncertain significance (Sep 30, 2021)
11-5778434-C-T		not specified	Uncertain significance (Jan 23, 2024)
11-5778438-G-A		not specified	Uncertain significance (Aug 04, 2023)
11-5778447-A-G		not specified	Uncertain significance (Feb 16, 2023)
11-5778511-T-C		not specified	Uncertain significance (Mar 01, 2023)
11-5778514-T-C		not specified	Uncertain significance (Feb 21, 2024)
11-5778526-G-A		not specified	Likely benign (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR52N5	protein_coding	protein_coding	ENST00000317093	1	1034

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000528	0.268	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.178	188	181	1.04	0.00000905	2120
Missense in Polyphen		55	52.275	1.0521		702
Synonymous	-0.0994	66	65.0	1.02	0.00000311	681
Loss of Function	-0.326	6	5.20	1.15	2.15e-7	78

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: 0.0757

Intolerance Scores

• loftool: 0.707
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.0579
• hipred: N
• hipred_score: 0.170
• ghis: 0.358

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0119

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr669

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