OPRD1
opioid receptor delta 1, the group of Opioid receptors
Basic information
Region (hg38): 1:28812170-28871267
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | 17 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 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) | ||
| 1-28812418-A-G | not specified | Uncertain significance (Dec 03, 2024) | ||
| 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) | ||
| 1-28859139-C-T | not specified | Uncertain significance (Aug 20, 2024) | ||
| 1-28859204-C-T | not specified | Uncertain significance (Nov 30, 2021) | ||
| 1-28859283-T-A | not specified | Uncertain significance (Jul 02, 2024) | ||
| 1-28859294-C-T | not specified | Uncertain significance (Sep 09, 2024) | ||
| 1-28859301-G-A | not specified | Uncertain significance (May 10, 2024) | ||
| 1-28862747-G-A | not specified | Uncertain significance (Jan 03, 2022) | ||
| 1-28862862-A-G | not specified | Uncertain significance (Sep 14, 2022) | ||
| 1-28862919-A-G | not specified | Uncertain significance (Mar 15, 2024) | ||
| 1-28862975-G-T | not specified | Uncertain significance (Jun 25, 2024) | ||
| 1-28862987-G-A | not specified | Uncertain significance (Apr 09, 2024) | ||
| 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-A | not specified | Uncertain significance (Jun 04, 2024) | ||
| 1-28863246-C-T | not specified | Uncertain significance (Mar 06, 2023) | ||
| 1-28863258-G-A | not specified | Uncertain significance (Dec 22, 2023) |
GnomAD
Source:
| 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:
- 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