OPN5

opsin 5, the group of Opsin receptors

Basic information

Region (hg38): 6:47781982-47832780

Previous symbols: [ "TMEM13" ]

Links

ENSG00000124818 ∙ NCBI:221391 ∙ OMIM:609042 ∙ HGNC:19992 ∙ Uniprot:Q6U736 ∙ 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 OPN5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OPN5 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
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	1

Variants in OPN5

This is a list of pathogenic ClinVar variants found in the OPN5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-47782091-C-A		not specified	Uncertain significance (Apr 09, 2024)
6-47782118-C-T		not specified	Uncertain significance (Dec 13, 2022)
6-47786593-T-C		not specified	Uncertain significance (Jan 20, 2023)
6-47791834-T-C		not specified	Uncertain significance (Dec 27, 2022)
6-47795405-A-C		not specified	Uncertain significance (Nov 11, 2024)
6-47795442-C-T		not specified	Uncertain significance (Aug 14, 2024)
6-47795477-G-C		not specified	Uncertain significance (Feb 02, 2024)
6-47795524-G-T			Benign (Dec 31, 2019)
6-47808158-C-T		not specified	Uncertain significance (Dec 04, 2024)
6-47808187-G-A		not specified	Uncertain significance (Jul 14, 2023)
6-47811717-G-C		not specified	Uncertain significance (Sep 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OPN5	protein_coding	protein_coding	ENST00000371211	7	50799

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.860	0.140	125723	0	6	125729	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.78	128	199	0.645	0.0000106	2275
Missense in Polyphen		32	73.275	0.43671		828
Synonymous	-0.00210	80	80.0	1.00	0.00000501	720
Loss of Function	3.48	3	19.6	0.153	0.00000107	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000368	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: 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: 0.151

Intolerance Scores

• loftool: 0.346
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

• pHI: 0.278
• hipred: Y
• hipred_score: 0.717
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.401

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Opn5
• Phenotype: vision/eye phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

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