OPN4

opsin 4, the group of Opsin receptors

Basic information

Region (hg38): 10:86654517-86666460

Links

ENSG00000122375 ∙ NCBI:94233 ∙ OMIM:606665 ∙ HGNC:14449 ∙ Uniprot:Q9UHM6 ∙ 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 OPN4 gene.

• Inborn genetic diseases (27 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OPN4 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			24	3	1	28
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	24	6	3

Variants in OPN4

This is a list of pathogenic ClinVar variants found in the OPN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-86654905-G-A		not specified	Likely benign (Nov 19, 2022)
10-86656234-C-A		not specified	Uncertain significance (Mar 29, 2022)
10-86656236-G-A		not specified	Uncertain significance (Jun 05, 2023)
10-86657207-T-G			Likely benign (Jun 01, 2022)
10-86658034-G-A		not specified	Uncertain significance (Feb 07, 2023)
10-86658061-T-G		not specified	Uncertain significance (Jun 22, 2023)
10-86658117-G-C		not specified	Uncertain significance (Nov 15, 2021)
10-86658138-T-C		not specified	Uncertain significance (Aug 08, 2023)
10-86658580-G-A		not specified	Uncertain significance (Jan 08, 2024)
10-86658598-G-A		not specified	Uncertain significance (Jun 29, 2023)
10-86658604-C-T		not specified	Likely benign (Nov 17, 2022)
10-86658613-G-A		not specified	Uncertain significance (Jan 09, 2024)
10-86658619-C-T		not specified	Uncertain significance (Mar 21, 2023)
10-86658639-G-A		not specified	Uncertain significance (Dec 09, 2023)
10-86658639-G-C		not specified	Uncertain significance (Dec 06, 2022)
10-86659330-G-A		not specified	Uncertain significance (Mar 16, 2022)
10-86659362-G-A		not specified	Uncertain significance (May 17, 2023)
10-86659377-A-G		not specified	Uncertain significance (Jan 16, 2024)
10-86659911-G-A		not specified	Uncertain significance (Oct 03, 2022)
10-86659948-G-A		not specified	Uncertain significance (Sep 01, 2021)
10-86659953-C-T		not specified	Uncertain significance (Jan 23, 2023)
10-86660001-C-T		not specified	Uncertain significance (Oct 06, 2022)
10-86660010-G-A		not specified	Uncertain significance (Dec 11, 2023)
10-86660041-C-T		not specified	Uncertain significance (Jan 03, 2024)
10-86660050-C-G		not specified	Uncertain significance (Jul 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OPN4	protein_coding	protein_coding	ENST00000372071	11	12292

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.01e-13	0.0756	125179	1	568	125748	0.00227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.479	334	310	1.08	0.0000196	3120
Missense in Polyphen		114	112.1	1.017		1182
Synonymous	-0.259	131	127	1.03	0.00000848	1021
Loss of Function	0.485	20	22.5	0.890	9.61e-7	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00200	0.00200
Ashkenazi Jewish	0.00	0.00
East Asian	0.000601	0.000598
Finnish	0.00471	0.00472
European (Non-Finnish)	0.00300	0.00299
Middle Eastern	0.000601	0.000598
South Asian	0.00148	0.00147
Other	0.00196	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Photoreceptor required for regulation of circadian rhythm. Contributes to pupillar reflex and other non-image forming responses to light. May be able to isomerize covalently bound all- trans retinal back to 11-cis retinal (By similarity). {ECO:0000250, ECO:0000269|PubMed:10632589, ECO:0000269|PubMed:15674244}.
• Pathway: GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Opsins;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.179

Intolerance Scores

• loftool: 0.923
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.69

Haploinsufficiency Scores

• pHI: 0.0990
• hipred: N
• hipred_score: 0.367
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.102

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Opn4
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); vision/eye phenotype; normal phenotype

Zebrafish Information Network

• Gene name: opn4a
• Affected structure: phototaxis
• Phenotype tag: abnormal
• Phenotype quality: process quality

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;visual perception;phototransduction;detection of visible light;protein-chromophore linkage;regulation of circadian rhythm;rhythmic process;cellular response to light stimulus
• Cellular component: integral component of plasma membrane;integral component of membrane;photoreceptor disc membrane
• Molecular function: 11-cis retinal binding;G protein-coupled photoreceptor activity