OR2J3
protein-codingolfactory receptor family 2 subfamily J member 3, the group of Olfactory receptors, family 2
Gene summary
This gene encodes a G-protein-coupled receptor (GPCR) that functions as an olfactory receptor. Olfactory receptors interact with odorant molecules in the nose to initiate a neuronal response that triggers the perception of a smell. The protein encoded by this gene responds to cis-3-hexen-1-ol, which is released by wounded plants, including cut grass. This gene is situated in a cluster of similar olfactory-receptor coding genes on chromosome 6. [provided by RefSeq, May 2013]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to OR2J3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001005216.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 46 | 3 | 49 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 46 | 3 | 0 | 49 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001005216.2 | 1 | MANE Select | |
| Ensembl | ENSP00000492961.1 | 1 | MANE Select | |
| Ensembl | ENSP00000366374.1 | 1 | Standard | |
| Ensembl | ENSP00000493439.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Olfactory transduction - Homo sapiens (human)
- Olfactory receptor activity
- GPCRs, Class A Rhodopsin-like
- Signaling by GPCR
- Signal Transduction
Biological Process
- G protein-coupled receptor signaling pathway
- detection of chemical stimulus involved in sensory perception of smell
Molecular Function
- G protein-coupled receptor activity
- olfactory receptor activity
Cellular Component
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000377169
- Coding exons
- 1
- Length
- 936
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.200 | 154 | 161 | 0.956 | 0.00000796 | 2001 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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}.;
Intolerance Scores
- LoFtool
- 0.506
- RVIS EVS
- 0.82
- RVIS percentile EVS
- 87.87
Essentials
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0331
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |