OPRL1

opioid related nociceptin receptor 1, the group of Opioid receptors

Basic information

Region (hg38): 20:64080081-64100643

Links

ENSG00000125510 ∙ NCBI:4987 ∙ OMIM:602548 ∙ HGNC:8155 ∙ Uniprot:P41146 ∙ 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 OPRL1 gene.

• Inborn genetic diseases (21 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OPRL1 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					3	3
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			13	1		14
Total	0	0	20	1	3

Variants in OPRL1

This is a list of pathogenic ClinVar variants found in the OPRL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-64083423-T-G		not specified	Uncertain significance (Jul 25, 2023)
20-64083424-C-G		not specified	Uncertain significance (Nov 14, 2023)
20-64083564-T-C		not specified	Uncertain significance (Sep 27, 2021)
20-64083566-C-G		not specified	Uncertain significance (Aug 22, 2023)
20-64083569-G-A		not specified	Uncertain significance (Sep 16, 2021)
20-64083585-C-T		not specified	Uncertain significance (Jul 19, 2023)
20-64083605-G-A		not specified	Uncertain significance (Feb 27, 2024)
20-64083656-G-T		not specified	Uncertain significance (Aug 13, 2021)
20-64083674-T-C		not specified	Uncertain significance (Nov 13, 2023)
20-64083684-T-A		not specified	Uncertain significance (Jul 13, 2021)
20-64083697-C-G		not specified	Uncertain significance (Jun 23, 2023)
20-64083910-C-T		not specified	Uncertain significance (Sep 23, 2023)
20-64083922-G-T		not specified	Uncertain significance (Nov 23, 2021)
20-64083946-C-T		not specified	Uncertain significance (Dec 15, 2023)
20-64083954-C-A		not specified	Uncertain significance (Sep 13, 2023)
20-64083963-G-A		not specified	Likely benign (Jun 16, 2023)
20-64083993-G-T		not specified	Uncertain significance (Feb 03, 2022)
20-64084065-G-A		not specified	Uncertain significance (Feb 05, 2024)
20-64084105-G-A		not specified	Uncertain significance (Apr 25, 2022)
20-64092838-G-A		not specified	Uncertain significance (Oct 12, 2021)
20-64092842-G-C		not specified	Uncertain significance (Mar 29, 2022)
20-64092910-G-A		not specified	Uncertain significance (Jul 31, 2023)
20-64097894-C-T		not specified	Uncertain significance (Nov 08, 2022)
20-64097919-G-A			Benign (Apr 23, 2018)
20-64098130-A-G		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OPRL1	protein_coding	protein_coding	ENST00000349451	3	20471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.482	0.514	125616	0	36	125652	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	187	250	0.748	0.0000179	2376
Missense in Polyphen		78	102.66	0.75981		1082
Synonymous	0.0135	117	117	0.998	0.00000860	837
Loss of Function	2.38	2	10.2	0.196	5.25e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000381	0.000381
South Asian	0.000294	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: G-protein coupled opioid receptor that functions as receptor for the endogenous neuropeptide nociceptin. Ligand binding causes a conformation change that triggers signaling via guanine nucleotide-binding proteins (G proteins) and modulates the activity of down-stream effectors. Signaling via G proteins mediates inhibition of adenylate cyclase activity and calcium channel activity. Arrestins modulate signaling via G proteins and mediate the activation of alternative signaling pathways that lead to the activation of MAP kinases. Plays a role in modulating nociception and the perception of pain. Plays a role in the regulation of locomotor activity by the neuropeptide nociceptin. {ECO:0000269|PubMed:11238602, ECO:0000269|PubMed:12568343, ECO:0000269|PubMed:22596163, ECO:0000269|PubMed:23086955, ECO:0000269|PubMed:8137918}.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);Peptide GPCRs;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.517
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.85

Haploinsufficiency Scores

• pHI: 0.101
• hipred: Y
• hipred_score: 0.538
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.685

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Oprl1
• Phenotype: homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); 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); hearing/vestibular/ear phenotype; normal phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway;neuropeptide signaling pathway;sensory perception;sensory perception of pain;response to estradiol;positive regulation of urine volume;opioid receptor signaling pathway;eating behavior;estrous cycle;negative regulation of blood pressure;positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway;positive regulation of gastric acid secretion;negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway;negative regulation of voltage-gated calcium channel activity;positive regulation of sensory perception of pain;regulation of locomotor rhythm
• Cellular component: plasma membrane;integral component of plasma membrane;cytoplasmic vesicle
• Molecular function: nociceptin receptor activity;G protein-coupled receptor activity;protein binding;protein C-terminus binding;peptide binding;neuropeptide binding