OPN1SW
protein-codingopsin 1, short wave sensitive, the group of Opsin receptors
Gene summary
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]
- BCP
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0008610
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0008610
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0008610
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0008610
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: Ophthalmologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to OPN1SW variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001385125.1. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 66 | 5 | 75 | ||
| missense | 157 | 15 | 2 | 174 | ||
| nonsense | 7 | 7 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 10 | 10 | ||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 184 | 81 | 7 | 272 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001372054.1 | 5 | MANE Select | |
| Ensembl | ENSP00000249389.3 | 5 | MANE Select | |
| Ensembl | ENSP00000802498.1 | 5 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| opn1sw1 | Danio rerio | Structure: horizontal cell Quality: amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- GPCRs, Class A Rhodopsin-like
- Signaling by GPCR
- Signal Transduction
- Opsins
- Class A/1 (Rhodopsin-like receptors)
Biological Process
- retinoid metabolic process
- signal transduction
- G protein-coupled receptor signaling pathway
- visual perception
- phototransduction
Molecular Function
- G protein-coupled photoreceptor activity
- signaling receptor activity
Cellular Component
- photoreceptor outer segment
- integral component of plasma membrane
- photoreceptor disc membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000249389
- Coding exons
- 5
- Length
- 3300
- Individuals with no LoFs
- 125689
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 58
- Defined
- 125748
- p
- 0.000235
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.00803 | 206 | 206 | 0.998 | 0.0000129 | 2273 |
| Missense (PolyPhen) | 63 | 70.819 | 0.88959 | 862 | ||
| Synonymous | -2.21 | 109 | 83.3 | 1.31 | 0.00000558 | 693 |
| Loss of Function | 2.12 | 5 | 13.4 | 0.374 | 5.78e-7 | 158 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00093 | 0.00093 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.00016 | 0.00016 | rare |
| South Asian | 0.00023 | 0.00020 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Visual pigments are the light-absorbing molecules that mediate vision. They consist of an apoprotein, opsin, covalently linked to cis-retinal.;
- Disease
- DISEASE: Tritan color blindness (CBT) [MIM:190900]: A disorder of vision characterized by a selective deficiency of blue spectral sensitivity. {ECO:0000269|PubMed:1386496, ECO:0000269|PubMed:1531728}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.328
Intolerance Scores
- LoFtool
- 0.767
- RVIS EVS
- -0.73
- RVIS percentile EVS
- 14.02
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.557
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |