OPN3

Chr 1

opsin 3

Also known as: ECPN, PPP1R116

NCBI Gene: 23596ENSG00000054277UniProt: Q9H1Y3OMIM: 606695

Opsin 3 encodes a G protein-coupled receptor that functions as a non-visual photoreceptor, binding retinal and responding to ultraviolet A and blue light to regulate melanogenesis, food intake via hypothalamic signaling, and various cellular processes including apoptosis and metabolism. The gene shows low constraint against loss-of-function variants (pLI 0.001, LOEUF 0.89), and currently no established human diseases are associated with OPN3 mutations. This opsin is expressed in multiple tissues including brain, skin, and testis, distinguishing it from the visual opsins found in the eye.

OMIMResearchSummary from RefSeq, UniProt
MultiplemechanismLOEUF 0.89
Clinical Summary— OPN3
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
65 unique Pathogenic / Likely Pathogenic· 168 VUS of 259 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
0.89LOEUF
pLI 0.001
Z-score 1.86
OE 0.48 (0.27–0.89)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.10Z-score
OE missense 0.79 (0.69–0.90)
168 obs / 213.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.48 (0.27–0.89)
0≤0.351.4
Missense OE0.79 (0.69–0.90)
0≤0.61.4
Synonymous OE0.99
0≤1.21.6
LoF obs/exp: 7 / 14.7Missense obs/exp: 168 / 213.0Syn Z: 0.07
DN
0.77top 25%
GOF
0.83top 10%
LOF
0.2581th %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

259 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic62
Likely Pathogenic3
VUS168
Likely Benign16
Benign1
62
Pathogenic
3
Likely Pathogenic
168
VUS
16
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
62
0
62
Likely Pathogenic
0
0
3
0
3
VUS
0
151
17
0
168
Likely Benign
0
13
1
2
16
Benign
0
0
0
1
1
Total0164833250

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

View in ClinVar →

Protein Context — Lollipop Plot

OPN3 · 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 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
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