RARRES2
retinoic acid receptor responder 2, the group of Receptor ligands
Basic information
Region (hg38): 7:150338317-150341662
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 RARRES2 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 | 1 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 1 | 1 |
Variants in RARRES2
This is a list of pathogenic ClinVar variants found in the RARRES2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-150338698-C-T | not specified | Uncertain significance (Apr 19, 2023) | ||
| 7-150338988-G-T | Benign (Aug 16, 2018) | |||
| 7-150339023-C-T | not specified | Uncertain significance (Jun 30, 2022) | ||
| 7-150340146-C-T | not specified | Uncertain significance (Jan 07, 2022) | ||
| 7-150340155-G-A | not specified | Uncertain significance (Jan 04, 2022) | ||
| 7-150340197-G-A | not specified | Uncertain significance (Apr 09, 2024) | ||
| 7-150340477-A-T | not specified | Uncertain significance (Jul 14, 2023) | ||
| 7-150340519-G-T | not specified | Uncertain significance (Jan 30, 2024) | ||
| 7-150340550-G-C | Benign (Jul 06, 2018) | |||
| 7-150340602-C-T | not specified | Likely benign (Oct 29, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RARRES2 | protein_coding | protein_coding | ENST00000466675 | 4 | 3356 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000272 | 0.335 | 125727 | 0 | 17 | 125744 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.385 | 80 | 90.3 | 0.886 | 0.00000492 | 1017 |
| Missense in Polyphen | 26 | 26.059 | 0.99775 | 354 | ||
| Synonymous | 1.94 | 22 | 37.0 | 0.595 | 0.00000177 | 324 |
| Loss of Function | 0.0786 | 7 | 7.23 | 0.968 | 3.09e-7 | 82 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000219 | 0.000219 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000616 | 0.0000615 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000675 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Adipocyte-secreted protein (adipokine) that regulates adipogenesis, metabolism and inflammation through activation of the chemokine-like receptor 1 (CMKLR1). Its other ligands include G protein-coupled receptor 1 (GPR1) and chemokine receptor-like 2 (CCRL2). Positively regulates adipocyte differentiation, modulates the expression of adipocyte genes involved in lipid and glucose metabolism and might play a role in angiogenesis, a process essential for the expansion of white adipose tissue. Also acts as a proinflammatory adipokine, causing an increase in secretion of proinflammatory and prodiabetic adipokines, which further impair adipose tissue metabolic function and have negative systemic effects including impaired insulin sensitivity, altered glucose and lipid metabolism, and a decrease in vascular function in other tissues. Can have both pro- and anti-inflammatory properties depending on the modality of enzymatic cleavage by different classes of proteases. Acts as a chemotactic factor for leukocyte populations expressing CMKLR1, particularly immature plasmacytoid dendritic cells, but also immature myeloid DCs, macrophages and natural killer cells. Exerts an anti-inflammatory role by preventing TNF/TNFA-induced VCAM1 expression and monocytes adhesion in vascular endothelial cells. The effect is mediated via inhibiting activation of NF-kappa-B and CRK/p38 through stimulation of AKT1/NOS3 signaling and nitric oxide production. Its dual role in inflammation and metabolism might provide a link between chronic inflammation and obesity, as well as obesity- related disorders such as type 2 diabetes and cardiovascular disease. Exhibits an antimicrobial function in the skin. {ECO:0000269|PubMed:14675762, ECO:0000269|PubMed:17635925, ECO:0000269|PubMed:17767914, ECO:0000269|PubMed:18242188, ECO:0000269|PubMed:20237162, ECO:0000269|PubMed:22634313, ECO:0000269|PubMed:23527010}.;
- Pathway
- Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis
(Consensus)
Recessive Scores
- pRec
- 0.119
Intolerance Scores
- loftool
- 0.503
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 53.19
Haploinsufficiency Scores
- pHI
- 0.305
- hipred
- N
- hipred_score
- 0.180
- ghis
- 0.516
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.122
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rarres2
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; endocrine/exocrine gland phenotype; immune system phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- retinoid metabolic process;in utero embryonic development;positive regulation of protein phosphorylation;platelet degranulation;chemotaxis;inflammatory response;insulin receptor signaling pathway;positive regulation of macrophage chemotaxis;antifungal humoral response;cell differentiation;innate immune response;positive regulation of fat cell differentiation;embryonic digestive tract development;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium;positive regulation of chemotaxis;regulation of lipid catabolic process;antifungal innate immune response
- Cellular component
- extracellular region;extracellular space;extracellular matrix;platelet dense granule lumen
- Molecular function
- signaling receptor binding;protein binding