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GeneBe

OPN1SW

opsin 1, short wave sensitive, the group of Opsin receptors

Basic information

Region (hg38): 7:128772484-128775794

Previous symbols: [ "BCP" ]

Links

ENSG00000128617NCBI:611OMIM:613522HGNC:1012Uniprot:P03999AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • blue color blindness (Supportive), mode of inheritance: AD
  • blue color blindness (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
TritanopiaADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic14946611; 1531728

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OPN1SW gene.

  • not provided (235 variants)
  • Inborn genetic diseases (20 variants)
  • Blue color blindness (5 variants)
  • not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OPN1SW gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
4
clinvar
52
clinvar
6
clinvar
62
missense
124
clinvar
8
clinvar
2
clinvar
134
nonsense
3
clinvar
3
start loss
1
clinvar
1
frameshift
6
clinvar
6
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
3
clinvar
3
splice region
?
0
non coding
?
2
clinvar
14
clinvar
4
clinvar
20
Total 0 0 144 74 12

Variants in OPN1SW

This is a list of pathogenic ClinVar variants found in the OPN1SW region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
7-128772544-T-C Uncertain significance (Mar 10, 2022)1509895
7-128772550-C-T Uncertain significance (Mar 20, 2022)2115402
7-128772564-C-A Benign (Jan 29, 2024)1167587
7-128772566-A-G Inborn genetic diseases Uncertain significance (Aug 02, 2021)2240721
7-128772567-G-A Likely benign (Jan 25, 2024)2711318
7-128772570-A-C Likely benign (Mar 25, 2020)1116696
7-128772571-G-A Uncertain significance (Feb 24, 2022)852775
7-128772574-G-A Uncertain significance (Aug 31, 2022)1036080
7-128772582-T-G Likely benign (Jul 19, 2022)1130650
7-128772592-G-T Uncertain significance (Feb 01, 2022)1478085
7-128772600-T-C Likely benign (May 02, 2022)1077815
7-128772602-T-C Inborn genetic diseases Uncertain significance (Oct 15, 2023)836919
7-128772605-C-G Uncertain significance (May 27, 2022)2100880
7-128772606-G-A Likely benign (Nov 19, 2023)1160419
7-128772612-A-G Likely benign (Oct 18, 2022)1905900
7-128772618-C-T Uncertain significance (Jun 22, 2022)1357380
7-128772632-A-C Uncertain significance (Aug 13, 2021)1396418
7-128772643-A-C Uncertain significance (Apr 29, 2022)1395268
7-128772646-A-G Uncertain significance (Aug 31, 2021)858901
7-128772646-A-T Uncertain significance (Mar 15, 2022)1485779
7-128772653-C-G Inborn genetic diseases Uncertain significance (Dec 16, 2021)2350167
7-128772654-T-C Uncertain significance (Oct 07, 2021)1398261
7-128772655-T-C Likely benign (Aug 05, 2022)1583167
7-128772656-G-A Uncertain significance (Aug 09, 2021)1373650
7-128772667-G-T Likely benign (Aug 20, 2022)1121794

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
OPN1SWprotein_codingprotein_codingENST00000249389 53300
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.02110.9641256891581257480.000235
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.008032062060.9980.00001292273
Missense in Polyphen6370.8190.88959862
Synonymous-2.2110983.31.310.00000558693
Loss of Function2.12513.40.3745.78e-7158

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009250.000925
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.00004700.0000462
European (Non-Finnish)0.0001590.000158
Middle Eastern0.0001090.000109
South Asian0.0002290.000196
Other0.000.00

dbNSFP

Source: dbNSFP

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.;
Pathway
GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Opsins;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;The retinoid cycle in cones (daylight vision);G alpha (i) signalling events;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

pRec
0.328

Intolerance Scores

loftool
0.767
rvis_EVS
-0.73
rvis_percentile_EVS
14.02

Haploinsufficiency Scores

pHI
0.100
hipred
N
hipred_score
0.400
ghis
0.556

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.557

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Opn1sw
Phenotype
vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Zebrafish Information Network

Gene name
opn1sw1
Affected structure
horizontal cell
Phenotype tag
abnormal
Phenotype quality
amount

Gene ontology

Biological process
retinoid metabolic process;signal transduction;G protein-coupled receptor signaling pathway;visual perception;phototransduction;detection of visible light;protein-chromophore linkage;cellular response to light stimulus
Cellular component
photoreceptor outer segment;integral component of plasma membrane;photoreceptor disc membrane
Molecular function
G protein-coupled photoreceptor activity;signaling receptor activity