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

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.

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	59	4	67
missense			134	8	2	144
nonsense			6			6
start loss			1			1
frameshift			7			7
inframe indel			1			1
splice donor/acceptor (+/-2bp)			4			4
splice region			5	6		11
non coding			3	16	4	23
Total	0	0	160	83	10

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)
7-128772550-C-T			Uncertain significance (Mar 20, 2022)
7-128772564-C-A		OPN1SW-related disorder	Benign (Jan 29, 2024)
7-128772564-C-T			Likely benign (Sep 01, 2023)
7-128772566-A-G		not specified	Uncertain significance (Aug 02, 2021)
7-128772567-G-A			Likely benign (Jan 25, 2024)
7-128772570-A-C			Likely benign (Mar 25, 2020)
7-128772571-G-A			Uncertain significance (Feb 24, 2022)
7-128772574-G-A			Uncertain significance (Aug 31, 2022)
7-128772582-T-G			Likely benign (Jul 19, 2022)
7-128772592-G-T			Uncertain significance (Feb 01, 2022)
7-128772600-T-C			Likely benign (May 02, 2022)
7-128772602-T-C		not specified	Uncertain significance (Oct 15, 2023)
7-128772605-C-G			Uncertain significance (May 27, 2022)
7-128772605-C-T			Uncertain significance (Aug 03, 2023)
7-128772606-G-A			Likely benign (Nov 19, 2023)
7-128772612-A-G			Likely benign (Jul 21, 2023)
7-128772613-T-G			Uncertain significance (Oct 11, 2023)
7-128772618-C-T			Uncertain significance (Jun 22, 2022)
7-128772632-A-C			Uncertain significance (May 19, 2021)
7-128772643-A-C			Uncertain significance (Apr 29, 2022)
7-128772646-A-G			Uncertain significance (Dec 24, 2019)
7-128772646-A-T			Uncertain significance (Mar 15, 2022)
7-128772653-C-G		not specified	Uncertain significance (Mar 14, 2023)
7-128772654-T-C			Uncertain significance (Oct 07, 2021)

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