OPN3

opsin 3, the group of Protein phosphatase 1 regulatory subunits|Opsin receptors

Basic information

Region (hg38): 1:241590101-241677376

Previous symbols: [ "ECPN" ]

Links

ENSG00000054277 ∙ NCBI:23596 ∙ OMIM:606695 ∙ HGNC:14007 ∙ Uniprot:Q9H1Y3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OPN3 gene.

• Inborn genetic diseases (44 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OPN3 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				2	1	3
missense			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			22	3		25
Total	0	0	41	7	1

Variants in OPN3

This is a list of pathogenic ClinVar variants found in the OPN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-241590214-C-G		not specified	Uncertain significance (Oct 13, 2021)
1-241590241-A-G		not specified	Uncertain significance (Dec 19, 2022)
1-241591963-A-G		not specified	Uncertain significance (Nov 18, 2022)
1-241592013-C-T		not specified	Uncertain significance (Jun 29, 2023)
1-241592023-A-G		not specified	Uncertain significance (Jan 26, 2022)
1-241592082-C-T		not specified	Likely benign (Feb 16, 2023)
1-241594687-C-T			Likely benign (Jan 01, 2023)
1-241597795-T-A		not specified	Uncertain significance (Sep 25, 2023)
1-241597817-T-C		not specified	Uncertain significance (Dec 28, 2022)
1-241597822-A-G		not specified	Uncertain significance (May 16, 2022)
1-241597843-C-A		not specified	Uncertain significance (Feb 27, 2023)
1-241597849-C-G		not specified	Uncertain significance (Sep 14, 2022)
1-241604291-C-T		not specified	Uncertain significance (Dec 19, 2023)
1-241604353-G-T			Likely benign (Apr 12, 2018)
1-241604358-C-T		not specified	Uncertain significance (Oct 25, 2023)
1-241604384-A-G		not specified	Uncertain significance (Nov 30, 2022)
1-241604400-C-T		not specified	Uncertain significance (Aug 16, 2021)
1-241604411-A-G		not specified	Uncertain significance (Dec 03, 2021)
1-241604420-C-G			Likely benign (Jan 01, 2023)
1-241604459-G-A		not specified	Uncertain significance (Nov 15, 2021)
1-241604483-G-A		not specified	Uncertain significance (Apr 18, 2023)
1-241604517-C-A		not specified	Uncertain significance (Jan 09, 2024)
1-241604553-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-241633926-T-C		not specified	Uncertain significance (Jan 26, 2023)
1-241633993-G-T		not specified	Uncertain significance (Feb 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OPN3	protein_coding	protein_coding	ENST00000366554	4	87275

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00128	0.964	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	168	213	0.789	0.0000107	2578
Missense in Polyphen		37	47.161	0.78454		647
Synonymous	0.0692	90	90.8	0.991	0.00000495	854
Loss of Function	1.86	7	14.7	0.476	8.43e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000175	0.000175
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000722	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in encephalic photoreception.
• Pathway: GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Opsins;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.201

Intolerance Scores

• loftool: 0.305
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.61

Haploinsufficiency Scores

• pHI: 0.184
• hipred: Y
• hipred_score: 0.590
• ghis: 0.455

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.497

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Opn3

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;phototransduction;detection of light stimulus;detection of visible light;protein-chromophore linkage;regulation of circadian rhythm;cellular response to light stimulus
• Cellular component: photoreceptor outer segment;integral component of plasma membrane;integral component of membrane
• Molecular function: G protein-coupled receptor activity;G protein-coupled photoreceptor activity;photoreceptor activity