OPN1SW opsin 1, short wave sensitive [Homo sapiens (human)] - Gene

Summary

Official Symbol: OPN1SWprovided by HGNC
Official Full Name: opsin 1, short wave sensitiveprovided by HGNC
Primary source: HGNC:HGNC:1012
See related: Ensembl:ENSG00000128617 MIM:613522; AllianceGenome:HGNC:1012
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: BCP; BOP; CBT
Summary: This gene belongs to the G-protein coupled receptor 1 family, opsin subfamily. It encodes the blue cone pigment gene which is one of three types of cone photoreceptors responsible for normal color vision. Defects in this gene are the cause of tritan color blindness (tritanopia). Affected individuals lack blue and yellow sensory mechanisms while retaining those for red and green. Defective blue vision is characteristic. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in heart (RPKM 1.6), appendix (RPKM 1.4) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7q32.1

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (128772485..128775794, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (130084638..130087947, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (128412539..128415848, complement)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Tritan color vision deficiency may be associated with an OPN1SW splicing defect and haploinsufficiency.
Title: Tritan color vision deficiency may be associated with an OPN1SW splicing defect and haploinsufficiency.
LVAVA haplotype of the OPN1LW gene and MVAVA haplotype of the OPN1MW gene cause apparently nonsyndromic high myopia in young patients but lead to progressive cone-rod dystrophy with deuteranopia and protanopia in middle-aged patients corresponding to a previously unknown disease course.
Title: Myopia and Late-Onset Progressive Cone Dystrophy Associate to LVAVA/MVAVA Exon 3 Interchange Haplotypes of Opsin Genes on Chromosome X.
Data suggest that insights into dimerization interface of red cone opsin should aid investigations of the structure and function of GPCR cell signaling.
Title: A G Protein-Coupled Receptor Dimerization Interface in Human Cone Opsins.
A novel homozygous PDE6C mutation was identified as the cause of ACHM. In addition, we identified an OPN1SW mutation in the sibling with complete achromatopsia.
Title: Congenital Achromatopsia and Macular Atrophy Caused by a Novel Recessive PDE6C Mutation (p.E591K).
Individuals with the T190I S-opsin mutation behaved as mild tritans at 12.3-92.3Td, but as tritanopes at 1.2-9.2Td, for both light-adapted and dark-adapted conditions. The results are consistent with the mutant opsin causing abnormal S-cone function.
Title: Substitution of isoleucine for threonine at position 190 of S-opsin causes S-cone-function abnormalities.
Observational study of genetic testing. (HuGE Navigator)
Title: Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip.
Results show that, although light absorption behaves differently in blue, green and red opsins, their low-frequency vibrational motions are similar.
Title: Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin.
Immunoreactivity to anti-OPN1SW antibodies was seen in the upper layer of human epidermis & reconstructed skin. The opsin mRNA was seen in total RNA from human skin. Neither immunoreactivity nor mRNA expression was seen in cultured human keratinocytes.
Title: Expressions of rod and cone photoreceptor-like proteins in human epidermis.
11-cis-retinol had no significant effect on the activity of human blue cone opsin
Title: The action of 11-cis-retinol on cone opsins and intact cone photoreceptors.
A novel mutation(prolin/leucine) in the short-wavelength-sensitive cone pigment gene associated with a tritan color vision defect.
Title: A novel mutation in the short-wavelength-sensitive cone pigment gene associated with a tritan color vision defect.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Blue color blindness MedGen: C0155017 OMIM: 190900 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study of primary tooth eruption identifies pleiotropic loci associated with height and craniofacial distances. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH66822 (e-PCR)
- UniSTS:75052

STS-M13299 (e-PCR)
- UniSTS:866

BCP (e-PCR)
- UniSTS:77748

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables G protein-coupled photoreceptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in G protein-coupled receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to UV-A	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to light stimulus	IBA Inferred from Biological aspect of Ancestor more info
involved_in detection of visible light	IEA Inferred from Electronic Annotation more info
involved_in phototransduction	IBA Inferred from Biological aspect of Ancestor more info
involved_in signal transduction	TAS Traceable Author Statement more info	PubMed
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cone photoreceptor outer segment	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in intercellular bridge	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor disc membrane	TAS Traceable Author Statement more info
located_in photoreceptor inner segment	IEA Inferred from Electronic Annotation more info
is_active_in photoreceptor outer segment	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: short-wave-sensitive opsin 1

Names: blue cone photoreceptor pigment; blue-sensitive opsin; opsin 1 (cone pigments), short-wave-sensitive

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_009094.1 RefSeqGene

Range

4997..8306

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001385125.1 → NP_001372054.1 short-wave-sensitive opsin 1

Status: REVIEWED

Source sequence(s)

AC024952

Consensus CDS

CCDS5806.2

UniProtKB/Swiss-Prot

P03999, Q13877

Related

ENSP00000249389.3, ENST00000249389.3

Conserved Domains (1) summary

cd15076
Location:32 → 311

7tmA_SWS1_opsin; short wave-sensitive 1 opsins, member of the class A family of seven-transmembrane G protein-coupled receptors

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

128772485..128775794 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060931.1 Alternate T2T-CHM13v2.0

Range

130084638..130087947 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001708.2: Suppressed sequence

Description

NM_001708.2: This RefSeq was removed because currently there is support for the transcript but not for the protein N-terminus.