OR52E2

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

Basic information

Region (hg38): 11:5058650-5059627

Links

ENSG00000176787 ∙ NCBI:119678 ∙ ∙ HGNC:14769 ∙ Uniprot:Q8NGJ4 ∙ 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 OR52E2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR52E2 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	0

Variants in OR52E2

This is a list of pathogenic ClinVar variants found in the OR52E2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-5058713-C-A		not specified	Uncertain significance (Jan 19, 2022)
11-5058868-T-C		not specified	Uncertain significance (Jul 06, 2021)
11-5058945-C-T		not specified	Likely benign (Dec 06, 2021)
11-5058946-G-A		not specified	Uncertain significance (Dec 07, 2021)
11-5058990-G-C		not specified	Uncertain significance (Jun 22, 2024)
11-5059023-A-G		not specified	Uncertain significance (Mar 28, 2024)
11-5059066-G-A		not specified	Uncertain significance (Aug 04, 2021)
11-5059071-A-T		not specified	Uncertain significance (Oct 17, 2023)
11-5059106-A-T		not specified	Uncertain significance (Mar 01, 2024)
11-5059113-C-T		not specified	Uncertain significance (Aug 16, 2021)
11-5059128-C-T		not specified	Uncertain significance (Feb 28, 2023)
11-5059186-G-A		not specified	Uncertain significance (Feb 21, 2024)
11-5059212-G-A		not specified	Uncertain significance (Dec 28, 2023)
11-5059249-C-T		not specified	Uncertain significance (Mar 18, 2024)
11-5059261-C-A		not specified	Uncertain significance (Oct 20, 2023)
11-5059348-T-C		not specified	Uncertain significance (May 23, 2024)
11-5059351-C-T		not specified	Uncertain significance (Dec 14, 2021)
11-5059356-A-C		not specified	Uncertain significance (Nov 07, 2022)
11-5059398-G-T		not specified	Uncertain significance (Jun 03, 2024)
11-5059411-C-T		not specified	Uncertain significance (Dec 06, 2021)
11-5059422-G-A		not specified	Uncertain significance (Oct 06, 2021)
11-5059454-G-C		not specified	Uncertain significance (Mar 07, 2024)
11-5059485-A-G		not specified	Uncertain significance (Sep 01, 2021)
11-5059511-G-C		not specified	Uncertain significance (Jul 06, 2022)
11-5059521-A-G		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR52E2	protein_coding	protein_coding	ENST00000321522	1	978

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0962	0.781	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.915	211	177	1.19	0.00000860	2120
Missense in Polyphen		48	50.607	0.94848		722
Synonymous	0.290	59	61.9	0.953	0.00000285	654
Loss of Function	1.18	2	4.77	0.419	2.85e-7	65

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: 0.0891

Intolerance Scores

• loftool: 0.760
• rvis_EVS: 2.44
• rvis_percentile_EVS: 98.56

Haploinsufficiency Scores

• pHI: 0.0562
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0143

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr589

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