OR13A1

Chr 10

olfactory receptor family 13 subfamily A member 1

NCBI Gene: 79290ENSG00000256574UniProt: Q8NGR1

OR13A1 encodes an olfactory receptor that recognizes and transduces odorant signals through G-protein-coupled receptor mechanisms in nasal sensory neurons. This gene has low constraint against loss-of-function variants (pLI 0.002, LOEUF 1.43), and no Mendelian diseases have been definitively associated with OR13A1 mutations in current medical literature.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
0
Pubs (1 yr)
13
P/LP submissions
0%
P/LP missense
1.43
LOEUF
Multiple*
Mechanism· predicted
Clinical Summary— OR13A1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
13 unique Pathogenic / Likely Pathogenic· 69 VUS of 94 total submissions
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.43LOEUF
pLI 0.002
Z-score 0.78
OE 0.69 (0.36–1.43)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-1.10Z-score
OE missense 1.22 (1.10–1.36)
243 obs / 199.3 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.69 (0.36–1.43)
0≤0.351.4
Missense OE1.22 (1.10–1.36)
0≤0.61.4
Synonymous OE1.33
0≤1.21.6
LoF obs/exp: 5 / 7.3Missense obs/exp: 243 / 199.3Syn Z: -2.53
DN
0.84top 10%
GOF
0.83top 10%
LOF
0.1499th %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

94 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic11
Likely Pathogenic2
VUS69
Likely Benign6
Benign1
11
Pathogenic
2
Likely Pathogenic
69
VUS
6
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
11
0
11
Likely Pathogenic
0
0
2
0
2
VUS
0
67
2
0
69
Likely Benign
0
4
1
1
6
Benign
0
0
1
0
1
Total07117189

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

View in ClinVar →

Protein Context — Lollipop Plot

OR13A1 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
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