OPRD1

opioid receptor delta 1, the group of Opioid receptors

Basic information

Region (hg38): 1:28812169-28871267

Links

ENSG00000116329 ∙ NCBI:4985 ∙ OMIM:165195 ∙ HGNC:8153 ∙ Uniprot:P41143 ∙ 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 OPRD1 gene.

• Inborn genetic diseases (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OPRD1 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						0
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in OPRD1

This is a list of pathogenic ClinVar variants found in the OPRD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-28812396-C-T		not specified	Uncertain significance (Aug 30, 2022)
1-28812424-C-T		not specified	Uncertain significance (Jan 31, 2023)
1-28812442-C-G		not specified	Uncertain significance (Jun 22, 2023)
1-28812454-C-T		not specified	Uncertain significance (Dec 13, 2021)
1-28812504-C-T		not specified	Uncertain significance (Apr 18, 2023)
1-28812576-C-G		not specified	Uncertain significance (Jan 10, 2023)
1-28859033-C-A		not specified	Uncertain significance (Dec 13, 2022)
1-28859064-C-T		not specified	Uncertain significance (Dec 02, 2022)
1-28859122-G-C		not specified	Uncertain significance (Dec 19, 2022)
1-28859204-C-T		not specified	Uncertain significance (Nov 30, 2021)
1-28862747-G-A		not specified	Uncertain significance (Jan 03, 2022)
1-28862862-A-G		not specified	Uncertain significance (Sep 14, 2022)
1-28862975-G-T		not specified	Uncertain significance (Apr 12, 2022)
1-28863204-G-A		not specified	Uncertain significance (May 18, 2023)
1-28863231-G-A		not specified	Uncertain significance (Feb 22, 2023)
1-28863246-C-T		not specified	Uncertain significance (Mar 06, 2023)
1-28863258-G-A		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OPRD1	protein_coding	protein_coding	ENST00000234961	3	51555

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00332	0.842	125707	1	39	125747	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	169	238	0.711	0.0000163	2332
Missense in Polyphen		55	84.998	0.64707		855
Synonymous	0.951	98	111	0.885	0.00000835	797
Loss of Function	1.19	5	8.80	0.568	3.77e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000431	0.000424
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000481	0.0000462
European (Non-Finnish)	0.0000996	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.000602	0.000555
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: G-protein coupled receptor that functions as receptor for endogenous enkephalins and for a subset of other opioids. Ligand binding causes a conformation change that triggers signaling via guanine nucleotide-binding proteins (G proteins) and modulates the activity of down-stream effectors, such as adenylate cyclase. Signaling leads to the inhibition of adenylate cyclase activity. Inhibits neurotransmitter release by reducing calcium ion currents and increasing potassium ion conductance. Plays a role in the perception of pain and in opiate-mediated analgesia. Plays a role in developing analgesic tolerance to morphine. {ECO:0000269|PubMed:22184124, ECO:0000269|PubMed:7808419, ECO:0000269|PubMed:8201839}.
• Pathway: Sphingolipid signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Peptide GPCRs;Interleukin-4 and 13 signaling;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)

Recessive Scores

• pRec: 0.346

Intolerance Scores

• loftool: 0.328
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.389
• hipred: Y
• hipred_score: 0.745
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.598

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Oprd1
• Phenotype: 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); 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: obsolete protein import into nucleus, translocation;immune response;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway;phospholipase C-activating G protein-coupled receptor signaling pathway;neuropeptide signaling pathway;adult locomotory behavior;negative regulation of gene expression;cytokine-mediated signaling pathway;negative regulation of protein oligomerization;positive regulation of CREB transcription factor activity;positive regulation of peptidyl-serine phosphorylation;opioid receptor signaling pathway;eating behavior;regulation of mitochondrial membrane potential;regulation of calcium ion transport;regulation of sensory perception of pain;cellular response to growth factor stimulus;cellular response to hypoxia;cellular response to toxic substance
• Cellular component: plasma membrane;integral component of plasma membrane;integral component of synaptic vesicle membrane;intrinsic component of plasma membrane;dendrite membrane;axon terminus;membrane raft;spine apparatus;neuronal dense core vesicle;integral component of presynaptic membrane;integral component of postsynaptic density membrane
• Molecular function: G protein-coupled receptor activity;opioid receptor activity;protein binding;receptor serine/threonine kinase binding;enkephalin receptor activity;peptide binding;neuropeptide binding