OR13J1

Chr 9

olfactory receptor family 13 subfamily J member 1

Also known as: OR9-2

NCBI Gene: 392309ENSG00000168828UniProt: Q8NGT2

OR13J1 encodes an olfactory receptor that binds odorant molecules in the nose and initiates G protein-coupled signaling to trigger smell perception. This gene is not associated with any known pediatric neurogenetic disorders. The gene shows no evidence of evolutionary constraint, with variants that disrupt protein function being well-tolerated in the general population.

ResearchSummary from RefSeq, UniProt
MultiplemechanismLOEUF 1.90
Clinical Summary— OR13J1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
73 unique Pathogenic / Likely Pathogenic· 63 VUS of 143 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
1.90LOEUF
pLI 0.000
Z-score -0.65
OE 1.30 (0.71–1.90)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.34Z-score
OE missense 1.07 (0.95–1.21)
198 obs / 184.9 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE1.30 (0.71–1.90)
0≤0.351.4
Missense OE1.07 (0.95–1.21)
0≤0.61.4
Synonymous OE1.00
0≤1.21.6
LoF obs/exp: 7 / 5.4Missense obs/exp: 198 / 184.9Syn Z: -0.03
DN
0.81top 10%
GOF
0.81top 10%
LOF
0.1894th %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

143 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic64
Likely Pathogenic9
VUS63
Likely Benign7
64
Pathogenic
9
Likely Pathogenic
63
VUS
7
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
64
0
64
Likely Pathogenic
0
0
9
0
9
VUS
0
55
8
0
63
Likely Benign
0
7
0
0
7
Benign
0
0
0
0
0
Total062810143

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

View in ClinVar →

Protein Context — Lollipop Plot

OR13J1 · 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 ↗
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