OR13A1
protein-codingolfactory receptor family 13 subfamily A member 1, the group of Olfactory receptors, family 13
Gene summary
Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.3 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 OR13A1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001004297.3. 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 | 1 | 1 | ||||
| missense | 69 | 4 | 73 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 69 | 5 | 0 | 74 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001004297.2 | 1 | MANE Select | |
| Ensembl | ENSP00000451950.1 | 1 | MANE Select | |
| Ensembl | ENSP00000363522.2 | 1 | Standard | |
| Ensembl | ENSP00000363522.2 | 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
- Signaling by GPCR
- Signal Transduction
- Olfactory Signaling Pathway
Biological Process
- G protein-coupled receptor signaling pathway
- sensory perception of smell
- detection of chemical stimulus involved in sensory perception of smell
Molecular Function
- G protein-coupled receptor activity
- olfactory receptor activity
- odorant binding
Cellular Component
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000553795
- Coding exons
- 1
- Length
- 12955
- Individuals with no LoFs
- 118369
- Homozygous LoFs
- 154
- Heterozygous LoFs
- 7224
- Defined
- 125747
- p
- 0.0298
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.10 | 243 | 199 | 1.22 | 0.0000115 | 2145 |
| Missense (PolyPhen) | 63 | 42.715 | 1.4749 | 591 | ||
| Synonymous | -2.53 | 126 | 94.7 | 1.33 | 0.00000688 | 676 |
| Loss of Function | 0.780 | 5 | 7.27 | 0.688 | 3.08e-7 | 87 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.055 | 0.055 | notable |
| Latino/Admixed American | 0.023 | 0.023 | notable |
| Ashkenazi Jewish | 0.067 | 0.068 | notable |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.025 | 0.025 | notable |
| European (Non-Finnish) | 0.035 | 0.035 | notable |
| South Asian | 0.012 | 0.012 | notable |
| Other | 0.043 | 0.043 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Odorant receptor. {ECO:0000305}.;
Intolerance Scores
- LoFtool
- 0.560
- RVIS EVS
- 0.38
- RVIS percentile EVS
- 75.51
Essentials
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.115
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |