OR3A1

Chr 17

olfactory receptor family 3 subfamily A member 1

Also known as: OLFRA03, OR17-40, OR17-82, OR40

NCBI Gene: 4994ENSG00000180090UniProt: P47881

OR3A1 encodes an olfactory receptor that binds odorant molecules and initiates G-protein coupled signaling cascades to trigger smell perception. This gene is not currently associated with any known Mendelian diseases or clinical phenotypes. The gene shows low constraint against loss-of-function variants, which is typical for olfactory receptor genes that exist in large, functionally redundant families.

ResearchSummary from RefSeq, UniProt
MultiplemechanismLOEUF 1.42
Clinical Summary— OR3A1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.02) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
40 unique Pathogenic / Likely Pathogenic· 79 VUS of 134 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.42LOEUF
pLI 0.023
Z-score 0.94
OE 0.56 (0.25–1.42)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.98Z-score
OE missense 1.21 (1.08–1.35)
213 obs / 176.5 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.56 (0.25–1.42)
0≤0.351.4
Missense OE1.21 (1.08–1.35)
0≤0.61.4
Synonymous OE1.05
0≤1.21.6
LoF obs/exp: 3 / 5.4Missense obs/exp: 213 / 176.5Syn Z: -0.33
DN
0.91top 5%
GOF
0.88top 5%
LOF
0.12100th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

134 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic38
Likely Pathogenic2
VUS79
Likely Benign13
Benign2
38
Pathogenic
2
Likely Pathogenic
79
VUS
13
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
38
0
38
Likely Pathogenic
0
0
2
0
2
VUS
0
68
11
0
79
Likely Benign
0
6
6
1
13
Benign
1
0
1
0
2
Total174581134

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

OR3A1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Studying Haloanisoles Interaction with Olfactory Receptors.
Silva Teixeira CS et al.·ACS Chem Neurosci
2016
Top 1 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients