OR52J3

olfactory receptor family 52 subfamily J member 3, the group of Olfactory receptors, family 52

Basic information

Region (hg38): 11:5046526-5047461

Links

ENSG00000205495 ∙ NCBI:119679 ∙ ∙ HGNC:14799 ∙ Uniprot:Q8NH60 ∙ 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 OR52J3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR52J3 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			24	2		26
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	2	0

Variants in OR52J3

This is a list of pathogenic ClinVar variants found in the OR52J3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-5046533-A-T		not specified	Uncertain significance (Aug 26, 2024)
11-5046587-G-A		not specified	Uncertain significance (Jul 14, 2021)
11-5046606-G-C		not specified	Uncertain significance (Jan 19, 2024)
11-5046616-G-C		not specified	Uncertain significance (Nov 01, 2022)
11-5046653-G-A		not specified	Uncertain significance (May 06, 2024)
11-5046677-T-C		not specified	Uncertain significance (Sep 06, 2022)
11-5046679-A-G		not specified	Uncertain significance (Aug 28, 2024)
11-5046701-A-G		not specified	Uncertain significance (Oct 09, 2024)
11-5046706-A-G		not specified	Uncertain significance (Feb 06, 2023)
11-5046770-G-A		not specified	Uncertain significance (Sep 12, 2023)
11-5046786-C-G		not specified	Uncertain significance (Mar 02, 2023)
11-5046862-G-A		not specified	Uncertain significance (Jan 10, 2023)
11-5046928-G-A		not specified	Likely benign (Oct 26, 2021)
11-5046928-G-T		not specified	Uncertain significance (Oct 24, 2023)
11-5046932-C-G		not specified	Uncertain significance (Aug 15, 2024)
11-5046967-A-T		not specified	Uncertain significance (Apr 18, 2024)
11-5046971-G-T		not specified	Uncertain significance (Jul 02, 2024)
11-5046983-G-A		not specified	Likely benign (Feb 14, 2023)
11-5046988-G-A		not specified	Uncertain significance (Nov 23, 2024)
11-5047024-C-T		not specified	Uncertain significance (Sep 12, 2024)
11-5047036-T-C		not specified	Uncertain significance (Mar 02, 2023)
11-5047074-C-A		not specified	Uncertain significance (Jul 14, 2023)
11-5047084-G-A		not specified	Uncertain significance (Oct 18, 2021)
11-5047106-T-A		not specified	Uncertain significance (Jul 06, 2021)
11-5047156-A-C		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR52J3	protein_coding	protein_coding	ENST00000380370	1	936

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000493	0.136	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.540	203	182	1.11	0.00000987	2014
Missense in Polyphen		58	52.255	1.1099		688
Synonymous	-2.54	93	66.6	1.40	0.00000358	662
Loss of Function	-0.796	7	5.07	1.38	2.11e-7	73

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: 0.0886

Intolerance Scores

• loftool: 0.645
• rvis_EVS: 1.82
• rvis_percentile_EVS: 97.01

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0487

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr592

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