OR52N2

olfactory receptor family 52 subfamily N member 2, the group of Olfactory receptors, family 52

Basic information

Region (hg38): 11:5808924-5821483

Links

ENSG00000180988

∙ NCBI:390077 ∙ ∙ HGNC:15228 ∙ Uniprot:Q8NGI0 ∙ 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 OR52N2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR52N2 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					1 clinvar	1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	1

Variants in OR52N2

This is a list of pathogenic ClinVar variants found in the OR52N2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-5821018-T-C			Benign (Jan 12, 2018)	789786

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR52N2	protein_coding	protein_coding	ENST00000317037	1	1035

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000182	0.286	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.196	194	186	1.04	0.00000956	2125
Missense in Polyphen		53	47.795	1.1089		655
Synonymous	-0.507	74	68.7	1.08	0.00000325	654
Loss of Function	-0.500	5	3.93	1.27	1.62e-7	61

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: 0.0481

Intolerance Scores

loftool: 0.856
rvis_EVS: 1.89
rvis_percentile_EVS: 97.29

Haploinsufficiency Scores

pHI: 0.0548
hipred: N
hipred_score: 0.123
ghis

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.143

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Olfr666
Phenotype

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