OPN3

Chr 1

opsin 3

Also known as: ECPN, PPP1R116

NCBI Gene: 23596ENSG00000054277UniProt: Q9H1Y3

Opsins are members of the guanine nucleotide-binding protein (G protein)-coupled receptor superfamily. In addition to the visual opsins, mammals possess several photoreceptive non-visual opsins that are expressed in extraocular tissues. This gene, opsin 3, is strongly expressed in brain and testis and weakly expressed in liver, placenta, heart, lung, skeletal muscle, kidney, and pancreas. The gene may also be expressed in the retina. The protein has the canonical features of a photoreceptive opsin protein. [provided by RefSeq, Jul 2008]

249
ClinVar variants
65
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— OPN3
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
65 Pathogenic / Likely Pathogenic· 167 VUS of 249 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.89LOEUF
pLI 0.001
Z-score 1.86
OE 0.48 (0.27–0.89)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.10Z-score
OE missense 0.79 (0.69–0.90)
168 obs / 213.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.48 (0.27–0.89)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.79 (0.69–0.90)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.99
0≤1.21.6
LoF obs/exp: 7 / 14.7Missense obs/exp: 168 / 213.0Syn Z: 0.07

ClinVar Variant Classifications

249 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic62
Likely Pathogenic3
VUS167
Likely Benign16
Benign1
62
Pathogenic
3
Likely Pathogenic
167
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
150
17
0
167
Likely Benign
0
13
1
2
16
Benign
0
0
0
1
1
Total0163833249

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.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
OPSIN 3; OPN3
MIM #606695 · *
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Expression of OPN3 in acral lentiginous melanoma and its associated with clinicohistopathologic features and prognosis.
Zeng W et al.·Immun Inflamm Dis
2021
The effects of missense OPN3 mutations in melanocytic lesions on protein structure and light-sensitive function.
Zhang W et al.·Exp Dermatol
2022
Integrated analysis of the prognostic and oncogenic roles of OPN3 in human cancers.
Zhang W et al.·BMC Cancer
2022
Identification of OPN3 as associated with non-syndromic oligodontia in a Japanese population.
Inagaki Y et al.·J Hum Genet
2021
Circadian rhythm genes contribute to the prognosis prediction and potential therapeutic target in gastric cancer.
Zhang C et al.·Sci Rep
2024
UVA Irradiation Promotes Melanoma Cell Proliferation Mediated by OPN3 Independently of ROS Production.
Zhang Y et al.·Pigment Cell Melanoma Res
2025
Opsin 3 expression in human Langerhans cell histiocytosis and its mediation of ELD-1 cellular function.
Ye T et al.·Eur J Dermatol
2023
Opsin 3 is a key regulator of ultraviolet A-induced photoageing in human dermal fibroblast cells.
Lan Y et al.·Br J Dermatol
2020
A Perspective on the Potential of Opsins as an Integral Mechanism of Photobiomodulation: It's Not Just the Eyes.
Liebert A et al.·Photobiomodul Photomed Laser Surg
2022Review
Construction of a four-mRNA prognostic signature with its ceRNA network in CESC.
Li L et al.·Sci Rep
2022
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools