OPN1SW

Chr 7AD

opsin 1, short wave sensitive

Also known as: BCP, BOP, CBT

NCBI Gene: 611ENSG00000128617UniProt: P03999

This gene belongs to the G-protein coupled receptor 1 family, opsin subfamily. It encodes the blue cone pigment gene which is one of three types of cone photoreceptors responsible for normal color vision. Defects in this gene are the cause of tritan color blindness (tritanopia). Affected individuals lack blue and yellow sensory mechanisms while retaining those for red and green. Defective blue vision is characteristic. [provided by RefSeq, Jul 2008]

Primary Disease Associations & Inheritance

Colorblindness, tritanMIM #190900
AD
UniProtTritan color blindness
349
ClinVar variants
25
Pathogenic / LP
0.02
pLI score
0
Active trials
Clinical Summary— OPN1SW
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.02) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
25 Pathogenic / Likely Pathogenic· 202 VUS of 349 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.
0.79LOEUF
pLI 0.021
Z-score 2.12
OE 0.37 (0.19–0.79)
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.
0.01Z-score
OE missense 1.00 (0.89–1.12)
206 obs / 206.3 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.0.37 (0.19–0.79)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.00 (0.89–1.12)
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.1.31
0≤1.21.6
LoF obs/exp: 5 / 13.4Missense obs/exp: 206 / 206.3Syn Z: -2.21

ClinVar Variant Classifications

349 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic25
VUS202
Likely Benign105
Benign12
Conflicting5
25
Pathogenic
202
VUS
105
Likely Benign
12
Benign
5
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
25
0
25
Likely Pathogenic
0
0
0
0
0
VUS
15
141
42
4
202
Likely Benign
0
8
32
65
105
Benign
0
2
6
4
12
Conflicting
—5
Total1515110573349

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

View in ClinVar →

Protein Context — Lollipop Plot

OPN1SW · 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

Colorblindness, tritan

MIM #190900

Molecular basis of disorder known

Autosomal dominant
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Identification and functional assays of single-nucleotide variants of opsins genes in melanocytic tumors.
Zhang W et al.·Pigment Cell Melanoma Res
2022Functional
Substitution of isoleucine for threonine at position 190 of S-opsin causes S-cone-function abnormalities.
Baraas RC et al.·Vision Res
2012
Congenital Achromatopsia and Macular Atrophy Caused by a Novel Recessive PDE6C Mutation (p.E591K).
Katagiri S et al.·Ophthalmic Genet
2015Case report
Genetic and clinical analysis in Chinese patients with retinitis pigmentosa caused by EYS mutations.
Sun Y et al.·Mol Genet Genomic Med
2020Case report
A degenerative retinal process in HIV-associated non-infectious retinopathy.
Kozak I et al.·PLoS One
2013
A Mouse Model with Ablated Asparaginase and Isoaspartyl Peptidase 1 (Asrgl1) Develops Early Onset Retinal Degeneration (RD) Recapitulating the Human Phenotype.
Biswas P et al.·Genes (Basel)
2022Functional
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