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:
- nephrogenic diabetes insipidus (Supportive), mode of inheritance: AD
- nephrogenic syndrome of inappropriate antidiuresis (Supportive), mode of inheritance: XL
- diabetes insipidus, nephrogenic, X-linked (Strong), mode of inheritance: XL
- nephrogenic syndrome of inappropriate antidiuresis (Strong), 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 (30 variants)
- Diabetes insipidus, nephrogenic, X-linked (13 variants)
- Nephrogenic diabetes insipidus (3 variants)
- Nephrogenic syndrome of inappropriate antidiuresis (2 variants)
- AVPR2-related disorder (2 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.
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 | 95 | 104 | ||||
| missense | 13 | 16 | 41 | 21 | 10 | 101 |
| nonsense | 14 | 16 | ||||
| start loss | 0 | |||||
| frameshift | 10 | 17 | ||||
| inframe indel | 3 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 3 | 3 | ||||
| non coding | 11 | 26 | ||||
| Total | 39 | 27 | 50 | 127 | 24 |
Variants in AVPR2
This is a list of pathogenic ClinVar variants found in the AVPR2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-153904993-G-GC | Benign (May 10, 2021) | |||
| X-153905098-G-C | Diabetes insipidus, nephrogenic, X-linked | Uncertain significance (Jan 13, 2018) | ||
| X-153905157-G-A | not specified • Diabetes insipidus, nephrogenic, X-linked • Diabetes insipidus, nephrogenic, X-linked;Nephrogenic syndrome of inappropriate antidiuresis | Benign/Likely benign (Jan 30, 2024) | ||
| X-153905163-C-T | Likely benign (May 22, 2023) | |||
| X-153905164-A-T | Diabetes insipidus, nephrogenic, X-linked • AVPR2-related disorder | Benign (Jan 31, 2024) | ||
| X-153905167-TC-T | Diabetes insipidus, nephrogenic, X-linked | Pathogenic (Apr 20, 2017) | ||
| X-153905181-C-T | Likely benign (Jan 24, 2023) | |||
| X-153905188-A-G | Likely benign (Feb 18, 2023) | |||
| X-153905288-A-G | Benign (May 11, 2021) | |||
| X-153905512-T-C | Likely benign (Nov 25, 2023) | |||
| X-153905518-C-T | Likely benign (Nov 30, 2023) | |||
| X-153905519-G-A | not specified | Likely benign (May 23, 2024) | ||
| X-153905519-G-C | Likely benign (Nov 25, 2023) | |||
| X-153905524-C-T | Likely benign (Nov 05, 2023) | |||
| X-153905526-T-G | not specified • Diabetes insipidus, nephrogenic, X-linked • Diabetes insipidus, nephrogenic, X-linked;Nephrogenic syndrome of inappropriate antidiuresis • Nephrogenic syndrome of inappropriate antidiuresis | Benign/Likely benign (Feb 01, 2024) | ||
| X-153905541-G-A | not specified • Diabetes insipidus, nephrogenic, X-linked | Benign (Jan 31, 2024) | ||
| X-153905542-G-A | Likely benign (Feb 05, 2023) | |||
| X-153905551-TCTGCCCAGCCTGCCCA-T | AVPR2-related disorder | Pathogenic (Sep 05, 2023) | ||
| X-153905575-C-T | Diabetes insipidus, nephrogenic, X-linked | Conflicting classifications of pathogenicity (Dec 14, 2023) | ||
| X-153905582-G-C | Inborn genetic diseases | Uncertain significance (Oct 12, 2022) | ||
| X-153905587-G-T | Diabetes insipidus, nephrogenic, X-linked | Uncertain significance (Jan 13, 2018) | ||
| X-153905590-A-C | Likely benign (Jan 29, 2024) | |||
| X-153905594-G-A | Inborn genetic diseases | Uncertain significance (Sep 07, 2022) | ||
| X-153905602-G-A | Likely benign (Apr 16, 2023) | |||
| X-153905607-C-T | Inborn genetic diseases | Uncertain significance (Feb 17, 2022) |
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 |
|---|---|---|---|---|---|---|
| 0.556 | 0.432 | 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
Haploinsufficiency Scores
- pHI
- 0.179
- hipred
- N
- hipred_score
- 0.445
- ghis
- 0.514
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 |
Mouse Genome Informatics
- Gene name
- Avpr2
- 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); growth/size/body region phenotype; homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype;
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