OPN1SW

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

Basic information

Region (hg38): 7:128772485-128775794

Previous symbols: [ "BCP" ]

Links

ENSG00000128617

∙ NCBI:611 ∙ OMIM:613522 ∙ HGNC:1012 ∙ Uniprot:P03999 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Tritanopia	AD	General	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	Ophthalmologic	14946611; 1531728

ClinVar

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

not_provided (270 variants)
not_specified (47 variants)
OPN1SW-related_disorder (8 variants)
Blue_color_blindness (5 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. These statistics are base on transcript: NM_001385125.1. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	61 clinvar	5 clinvar	70
missense			146 clinvar	15 clinvar	2 clinvar	163
nonsense			6 clinvar			6
start loss			1			1
frameshift			10 clinvar			10
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	172	76	7

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OPN1SW	protein_coding	protein_coding	ENST00000249389	5	3300

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0211	0.964	125689	1	58	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00803	206	206	0.998	0.0000129	2273
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000925	0.000925
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.000109	0.000109
South Asian	0.000229	0.000196
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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