OPN1MW2

opsin 1, medium wave sensitive 2, the group of Opsin receptors

Basic information

Region (hg38): X:154219756-154233286

Links

ENSG00000166160 ∙ NCBI:728458 ∙ ∙ HGNC:26952 ∙ Uniprot:P0DN77 ∙ 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 OPN1MW2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OPN1MW2 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			9	3		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	4	0

Variants in OPN1MW2

This is a list of pathogenic ClinVar variants found in the OPN1MW2 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-154224988-A-G		not specified	Uncertain significance (Mar 11, 2022)
X-154224989-T-C		not specified	Likely benign (Aug 30, 2021)
X-154225087-G-A		Deuteranomaly	Uncertain significance (Mar 31, 2019)
X-154225099-G-A		not specified	Uncertain significance (Aug 16, 2021)
X-154225126-G-A		not specified	Uncertain significance (Nov 03, 2023)
X-154225169-T-C		not specified	Uncertain significance (Dec 08, 2023)
X-154227239-A-C		not specified	Likely benign (Sep 01, 2021)
X-154230590-G-C		not specified	Uncertain significance (Jul 25, 2023)
X-154230635-T-C		not specified	Uncertain significance (Jun 11, 2021)
X-154230635-T-G		not specified	Uncertain significance (Jan 29, 2024)
X-154230656-G-A		not specified	Likely benign (Mar 01, 2023)
X-154230691-C-T			Likely benign (May 01, 2022)
X-154230696-C-T		not specified	Uncertain significance (Jul 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OPN1MW2	protein_coding	protein_coding	ENST00000369929	6	13531

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.245	0.652	110539	1	1	110541	0.00000905

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.352	51	58.6	0.870	0.00000463	2358
Missense in Polyphen		20	30.343	0.65914		984
Synonymous	0.0347	27	27.2	0.992	0.00000253	711
Loss of Function	1.19	1	3.34	0.300	2.11e-7	167

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000273	0.0000202
Middle Eastern	0.00	0.00
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. {ECO:0000250|UniProtKB:P04001}.
• Pathway: 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: 0.145

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

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: photoreceptor outer segment;integral component of plasma membrane
• Molecular function: G protein-coupled photoreceptor activity