OR2T4

Chr 1

olfactory receptor family 2 subfamily T member 4

Also known as: OR1-60, OR2T4Q

NCBI Gene: 127074ENSG00000196944UniProt: Q8NH00

OR2T4 encodes an olfactory receptor that binds odorant molecules and initiates G-protein-coupled signaling cascades to trigger smell perception. No disease associations have been established for mutations in this gene based on the available data. The gene shows tolerance to loss-of-function variants (pLI 0.19, LOEUF 0.94), which is consistent with the large redundancy typical of the olfactory receptor gene family.

ResearchSummary from RefSeq, UniProt
MultiplemechanismLOEUF 0.94
Clinical Summary— OR2T4
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.30) despite low pLI — interpret in context.
📋
ClinVar Variants
69 unique Pathogenic / Likely Pathogenic· 64 VUS of 148 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
0.94LOEUF
pLI 0.195
Z-score 1.69
OE 0.30 (0.12–0.94)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
-0.88Z-score
OE missense 1.19 (1.06–1.33)
211 obs / 177.9 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.30 (0.12–0.94)
0≤0.351.4
Missense OE1.19 (1.06–1.33)
0≤0.61.4
Synonymous OE1.26
0≤1.21.6
LoF obs/exp: 2 / 6.7Missense obs/exp: 211 / 177.9Syn Z: -1.67
DN
0.86top 5%
GOF
0.88top 5%
LOF
0.1697th %ile

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

GOFprediction above median
DNprediction 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

148 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic63
Likely Pathogenic6
VUS64
Likely Benign6
Benign9
63
Pathogenic
6
Likely Pathogenic
64
VUS
6
Likely Benign
9
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
63
0
63
Likely Pathogenic
0
0
6
0
6
VUS
0
43
21
0
64
Likely Benign
0
0
6
0
6
Benign
0
0
9
0
9
Total0431050148

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

View in ClinVar →

Protein Context — Lollipop Plot

OR2T4 · 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
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