AVPR2
arginine vasopressin receptor 2, the group of Arginine vasopressin and oxytocin receptors
Basic information
Region (hg38): X:153902531-153907166
Previous symbols: [ "DIR3", "DIR" ]
Links
Phenotypes
GenCC
Source:
- diabetes insipidus, nephrogenic, X-linked (Strong), mode of inheritance: XL
- nephrogenic syndrome of inappropriate antidiuresis (Strong), mode of inheritance: XL
- nephrogenic diabetes insipidus (Supportive), mode of inheritance: AD
- nephrogenic syndrome of inappropriate antidiuresis (Supportive), mode of inheritance: XL
- nephrogenic syndrome of inappropriate antidiuresis (Moderate), mode of inheritance: XL
- diabetes insipidus, nephrogenic, X-linked (Definitive), mode of inheritance: XL
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Diabetes insipidus 1, nephrogenic, X-linked; Nephrogenic syndrome of inappropriate antidiuresis | XL | Endocrine; Renal | In Diabetes insipidus, nephrogenic, X-linked, sequelae may be prevented with early genetic knowledge to allow management of electrolyte and fluid balances (eg, with specific diuretics) has been reported as potentially beneficial); In Nephrogenic syndrome of inappropriate antidiuresis, patients can have electrolyte and fluid imbalances, and management of these issues through initial fluid restriction and osmotic agents) have been reported to be beneficial | Endocrine; Renal | 13644230; 3970081; 3080575; 1356229; 1303271; 8104196; 9329382; 10477148; 15872203; 16845277; 22722264 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (248 variants)
- Diabetes_insipidus,_nephrogenic,_X-linked (129 variants)
- Nephrogenic_syndrome_of_inappropriate_antidiuresis (61 variants)
- Inborn_genetic_diseases (34 variants)
- not_specified (25 variants)
- Nephrogenic_diabetes_insipidus (21 variants)
- AVPR2-related_disorder (17 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the AVPR2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000054.7. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 7 | 101 | 6 | 114 | ||
| missense | 21 | 30 | 99 | 34 | 9 | 193 |
| nonsense | 16 | 1 | 1 | 18 | ||
| start loss | 0 | |||||
| frameshift | 23 | 15 | 38 | |||
| splice donor/acceptor (+/-2bp) | 4 | 4 | 8 | |||
| Total | 64 | 46 | 111 | 135 | 15 |
Highest pathogenic variant AF is 0.0000027537892
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| AVPR2 | protein_coding | protein_coding | ENST00000358927 | 3 | 4636 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 125386 | 0 | 1 | 125387 | 0.00000399 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.01 | 148 | 187 | 0.792 | 0.0000178 | 2337 |
| Missense in Polyphen | 47 | 81.69 | 0.57534 | 1143 | ||
| Synonymous | -1.10 | 91 | 78.6 | 1.16 | 0.00000710 | 851 |
| Loss of Function | 2.03 | 1 | 6.63 | 0.151 | 4.22e-7 | 99 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000722 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000722 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor for arginine vasopressin. The activity of this receptor is mediated by G proteins which activate adenylate cyclase. Involved in renal water reabsorption. {ECO:0000269|PubMed:19440390}.;
- Disease
- DISEASE: Diabetes insipidus, nephrogenic, X-linked (XNDI) [MIM:304800]: A disorder caused by the inability of the renal collecting ducts to absorb water in response to arginine vasopressin. Characterized by excessive water drinking (polydipsia), excessive urine excretion (polyuria), persistent hypotonic urine, and hypokalemia. {ECO:0000269|PubMed:10694923, ECO:0000269|PubMed:10770218, ECO:0000269|PubMed:11026555, ECO:0000269|PubMed:11232028, ECO:0000269|PubMed:11916004, ECO:0000269|PubMed:1303257, ECO:0000269|PubMed:1303271, ECO:0000269|PubMed:1356229, ECO:0000269|PubMed:16845277, ECO:0000269|PubMed:7560098, ECO:0000269|PubMed:7833930, ECO:0000269|PubMed:7984150, ECO:0000269|PubMed:7987330, ECO:0000269|PubMed:7999078, ECO:0000269|PubMed:8037205, ECO:0000269|PubMed:8045948, ECO:0000269|PubMed:8078903, ECO:0000269|PubMed:8267567, ECO:0000269|PubMed:8479490, ECO:0000269|PubMed:8514744, ECO:0000269|PubMed:9402087, ECO:0000269|PubMed:9452109, ECO:0000269|PubMed:9711877}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Vasopressin-regulated water reabsorption - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Vasopressin Regulation of Water Homeostasis;Peptide GPCRs;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;G alpha (s) signalling events;Vasopressin-like receptors;Peptide ligand-binding receptors;Transport of small molecules;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis;Arf6 trafficking events;Vasopressin regulates renal water homeostasis via Aquaporins;Aquaporin-mediated transport;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.589
Intolerance Scores
- loftool
- 0.104
- rvis_EVS
- 1.09
- rvis_percentile_EVS
- 91.85
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.731
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- regulation of systemic arterial blood pressure by vasopressin;positive regulation of systemic arterial blood pressure;renal water homeostasis;G protein-coupled receptor signaling pathway;adenylate cyclase-modulating G protein-coupled receptor signaling pathway;activation of adenylate cyclase activity;I-kappaB kinase/NF-kappaB signaling;excretion;hemostasis;positive regulation of cell population proliferation;positive regulation of gene expression;telencephalon development;positive regulation of protein ubiquitination;interferon-gamma production;cellular response to hormone stimulus;response to cytokine;negative regulation of urine volume;negative regulation of renal sodium excretion;positive regulation of vasoconstriction;membrane organization
- Cellular component
- endosome;endoplasmic reticulum;Golgi apparatus;plasma membrane;integral component of plasma membrane;integral component of membrane;clathrin-coated vesicle membrane
- Molecular function
- vasopressin receptor activity;protein binding