OR2J3

olfactory receptor family 2 subfamily J member 3, the group of Olfactory receptors, family 2

Basic information

Region (hg38): 6:29108058-29114770

Links

ENSG00000204701 ∙ NCBI:442186 ∙ OMIM:615016 ∙ HGNC:8261 ∙ Uniprot:O76001 ∙ 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 OR2J3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2J3 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			15	3		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	3	0

Variants in OR2J3

This is a list of pathogenic ClinVar variants found in the OR2J3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-29111967-T-C		not specified	Uncertain significance (Apr 28, 2023)
6-29111978-A-C		not specified	Likely benign (Nov 07, 2022)
6-29112010-G-A		not specified	Uncertain significance (Nov 29, 2023)
6-29112094-C-A		not specified	Uncertain significance (Nov 13, 2023)
6-29112227-A-G		C3HEX, ability to smell	Affects (Sep 01, 2012)
6-29112322-C-G		not specified	Uncertain significance (Jan 10, 2023)
6-29112414-G-A		not specified	Likely benign (May 24, 2023)
6-29112456-G-A		not specified	Uncertain significance (Feb 22, 2023)
6-29112497-A-T		not specified	Uncertain significance (Mar 24, 2023)
6-29112515-T-G		not specified	Uncertain significance (May 23, 2023)
6-29112525-T-A		not specified	Uncertain significance (Apr 28, 2022)
6-29112564-T-C		not specified	Likely benign (Dec 27, 2023)
6-29112567-G-A		C3HEX, ability to smell	Affects (Sep 01, 2012)
6-29112580-G-C		not specified	Uncertain significance (Dec 27, 2023)
6-29112620-T-C		not specified	Uncertain significance (Jan 26, 2022)
6-29112641-G-C		not specified	Uncertain significance (Feb 28, 2024)
6-29112698-T-G		not specified	Uncertain significance (Jan 05, 2022)
6-29112746-C-T		not specified	Uncertain significance (Mar 21, 2024)
6-29112762-T-C		not specified	Uncertain significance (Aug 16, 2021)
6-29112782-A-C		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2J3	protein_coding	protein_coding	ENST00000377169	1	936

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00985	0.834	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.200	154	161	0.956	0.00000796	2001
Missense in Polyphen		46	44.808	1.0266		629
Synonymous	-0.340	66	62.6	1.05	0.00000317	664
Loss of Function	1.14	4	7.32	0.546	4.86e-7	82

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 involved in the detection of the flavor compound cis-3-hexen-1-ol (C3HEX), a compound typically described as 'green grassy' or the smell of 'cut grass'. {ECO:0000269|PubMed:22714804}.
• Pathway: Olfactory transduction - Homo sapiens (human);Olfactory receptor activity;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.506
• rvis_EVS: 0.82
• rvis_percentile_EVS: 87.87

Haploinsufficiency Scores

• pHI: 0.0962
• hipred: N
• hipred_score: 0.112
• ghis: 0.396

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0331

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr137

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