OR52E4

olfactory receptor family 52 subfamily E member 4, the group of Olfactory receptors, family 52

Basic information

Region (hg38): 11:5880629-5887079

Links

ENSG00000180974 ∙ NCBI:390081 ∙ ∙ HGNC:15213 ∙ Uniprot:Q8NGH9 ∙ 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 OR52E4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR52E4 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in OR52E4

This is a list of pathogenic ClinVar variants found in the OR52E4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-5884344-G-C		not specified	Uncertain significance (Jun 18, 2021)
11-5884372-T-C		not specified	Uncertain significance (Nov 20, 2023)
11-5884375-G-T		not specified	Uncertain significance (Aug 22, 2023)
11-5884385-C-G		not specified	Uncertain significance (Jan 26, 2022)
11-5884446-A-G		not specified	Uncertain significance (Nov 19, 2022)
11-5884466-C-G		not specified	Uncertain significance (May 23, 2023)
11-5884491-A-T		not specified	Uncertain significance (Mar 14, 2023)
11-5884559-C-G		not specified	Uncertain significance (Aug 15, 2023)
11-5884590-C-G		not specified	Uncertain significance (Nov 17, 2022)
11-5884624-G-A		not specified	Uncertain significance (Dec 27, 2022)
11-5884636-T-C		not specified	Uncertain significance (Mar 14, 2024)
11-5884764-G-A		not specified	Uncertain significance (Mar 01, 2023)
11-5884768-C-T		not specified	Uncertain significance (May 02, 2024)
11-5884788-C-A		not specified	Uncertain significance (Jun 17, 2024)
11-5884791-C-T		not specified	Uncertain significance (Aug 10, 2021)
11-5884792-G-A		not specified	Uncertain significance (Oct 03, 2022)
11-5884821-C-T		not specified	Uncertain significance (Dec 17, 2023)
11-5884860-G-A		not specified	Uncertain significance (Dec 27, 2023)
11-5884867-C-A		not specified	Uncertain significance (Jun 09, 2022)
11-5884874-T-G		not specified	Uncertain significance (Jun 29, 2023)
11-5884893-G-A		not specified	Uncertain significance (Aug 22, 2023)
11-5885083-G-A		not specified	Uncertain significance (May 16, 2022)
11-5885131-T-C		not specified	Uncertain significance (Nov 08, 2022)
11-5885137-T-C		not specified	Uncertain significance (Feb 14, 2023)
11-5885146-C-A		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR52E4	protein_coding	protein_coding	ENST00000316987	1	1027

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.59e-7	0.0750	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.886	199	167	1.19	0.00000816	2054
Missense in Polyphen		45	55.034	0.81768		727
Synonymous	-1.24	72	59.8	1.20	0.00000274	645
Loss of Function	-1.11	8	5.26	1.52	3.10e-7	70

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: 0.0689

Intolerance Scores

• loftool: 0.769
• rvis_EVS: 1.71
• rvis_percentile_EVS: 96.46

Haploinsufficiency Scores

• pHI: 0.132
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0773

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr677

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