OPN1LW

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

Basic information

Region (hg38): X:154144243-154159032

Previous symbols: [ "CBBM", "RCP", "CBP" ]

Links

ENSG00000102076 ∙ NCBI:5956 ∙ OMIM:300822 ∙ HGNC:9936 ∙ Uniprot:P04000 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• blue cone monochromacy (Supportive), mode of inheritance: XL
• cone-rod dystrophy (Supportive), mode of inheritance: AD
• blue cone monochromacy (Definitive), mode of inheritance: XL
• red color blindness (Strong), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Colorblindness, partial, protan series; Blue cone monochromacy; Red cone polymorphism	XL (involving both OPN1 genes)	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	2847528; 2788922; 1881435; 1415215; 1302020; 8213841; 8792812; 10982039; 11772996; 12051694; 20579627; 23139274

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OPN1LW gene.

• not provided (2 variants)
• Cone monochromatism (2 variants)
• Protan defect (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OPN1LW 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				1	1	2
missense	1		9	4	2	16
nonsense	2					2
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	3	1	9	5	3

Variants in OPN1LW

This is a list of pathogenic ClinVar variants found in the OPN1LW region.

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

Position	Type	Phenotype	Significance	ClinVar
X-154144314-G-C		not specified	Uncertain significance (Sep 12, 2024)
X-154150664-G-T			Likely pathogenic (May 27, 2022)
X-154150770-C-T		not specified	Likely benign (Dec 22, 2023)
X-154150796-C-T			Uncertain significance (Mar 06, 2017)
X-154150812-G-A		Cone monochromatism	Pathogenic (Oct 05, 2021)
X-154150832-G-A		not specified	Uncertain significance (Dec 11, 2023)
X-154150858-C-T			Likely benign (Nov 01, 2022)
X-154150890-C-A			Likely benign (Apr 01, 2023)
X-154150897-C-G			Pathogenic (Mar 01, 2021)
X-154153009-G-A		not specified	Uncertain significance (Jul 14, 2024)
X-154153018-G-T		not specified	Uncertain significance (Mar 07, 2023)
X-154153041-G-A		Cone monochromatism	Benign (Sep 05, 2021)
X-154153043-G-T		Cone monochromatism	Benign (Sep 05, 2021)
X-154153044-G-A		not specified	Uncertain significance (Dec 06, 2024)
X-154153062-A-G		not specified	Benign (Mar 29, 2016)
X-154153068-G-G		RED CONE POLYMORPHISM • not specified	Benign (-)
X-154153075-T-C		not specified	Uncertain significance (Jul 05, 2024)
X-154154575-T-C		not specified	Uncertain significance (Feb 06, 2024)
X-154154587-G-A		not specified	Uncertain significance (Nov 21, 2024)
X-154154602-T-C		Cone monochromatism • Protan defect	Pathogenic (Oct 21, 2021)
X-154154630-C-T		not specified	Uncertain significance (Oct 05, 2023)
X-154154684-T-C			Likely benign (Oct 01, 2023)
X-154154701-A-C			Likely benign (Apr 01, 2022)
X-154154723-G-T		not specified	Uncertain significance (Nov 13, 2024)
X-154154725-C-G		not specified	Uncertain significance (Nov 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OPN1LW	protein_coding	protein_coding	ENST00000369951	6	14810

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.975	0.0246	124091	0	1	124092	0.00000403

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.466	126	142	0.890	0.0000121	2367
Missense in Polyphen		44	67.148	0.65527		1080
Synonymous	-0.186	65	63.1	1.03	0.00000621	724
Loss of Function	3.13	0	11.4	0.00	8.02e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000725	0.0000547
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000725	0.0000547
South Asian	0.00	0.00
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: Colorblindness, partial, protan series (CBP) [MIM:303900]: A color vision defect characterized by a dichromasy in which red and green are confused, with loss of luminance and shift of brightness and hue curves toward the short wave end of the spectrum. Dichromasy is due to the use of only two types of photoreceptors, blue plus red in deuteranopia and blue plus green in protanopia. {ECO:0000269|PubMed:12051694}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Blue cone monochromacy (BCM) [MIM:303700]: A rare X- linked congenital stationary cone dysfunction syndrome characterized by the absence of functional long wavelength- sensitive and medium wavelength-sensitive cones in the retina. Color discrimination is severely impaired from birth, and vision is derived from the remaining preserved blue (S) cones and rod photoreceptors. BCM typically presents with reduced visual acuity, pendular nystagmus, and photophobia. Patients often have myopia. {ECO:0000269|PubMed:8213841, ECO:0000269|PubMed:8666378}. 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)

Intolerance Scores

• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.3

Haploinsufficiency Scores

• pHI: 0.252
• hipred: N
• hipred_score: 0.431
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.675

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Opn1mw
• Phenotype: vision/eye phenotype

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;positive regulation of cytokinesis;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;photoreceptor activity