OPN1MW2

protein-coding

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

Gene summary

This gene encodes for a light absorbing visual pigment of the opsin gene family. The encoded protein is called green cone photopigment or medium-wavelength sensitive opsin. Opsins are G-protein coupled receptors with seven transmembrane domains, an N-terminal extracellular domain, and a C-terminal cytoplasmic domain. The long-wavelength opsin gene and multiple copies of the medium-wavelength opsin gene are tandemly arrayed on the X chromosome and frequent unequal recombination and gene conversion may occur between these sequences. X chromosomes may have fusions of the medium- and long-wavelength opsin genes or may have more than one copy of these genes. Defects in this gene are the cause of deutanopic colorblindness. [provided by RefSeq, Mar 2009]

MANE transcript

NM_001048181.3

Inheritance

—

ClinVar variants

U:19B:9

Top phenotype

Deuteranomaly

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chrX:154,219,756-154,233,286

External References & Databases

Ensembl (ENSG00000166160)

Transcript & Mutation Effects

hg38 • Region Span ~13.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OPN1MW2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 22

not providedTotal: 7

DeuteranomalyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001048181.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar		4
missense			19 clinvar	5 clinvar		24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	19	9	0	28

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001048181.3	RefSeq	NP_001041646.1	6	MANE Select
ENST00000369929.8	Ensembl	ENSP00000358945.4	6	MANE Select
ENST00000430419.1	Ensembl	ENSP00000403023.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signaling by GPCR
Signal Transduction
Opsins
Class A/1 (Rhodopsin-like receptors)
GPCR ligand binding

Biological Process

G protein-coupled receptor signaling pathway
visual perception
phototransduction
detection of visible light
protein-chromophore linkage

Molecular Function

G protein-coupled photoreceptor activity

Cellular Component

photoreceptor outer segment
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369929
Coding exons: 6
Length: 13531
Individuals with no LoFs: 110539
Homozygous LoFs: 1
Heterozygous LoFs: 1
Defined: 110541
p: 0.00000905

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.352	51	58.6	0.870	0.00000463	2358
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000020	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.145

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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