RXRB
retinoid X receptor beta, the group of Retinoid X receptors
Basic information
Region (hg38): 6:33193587-33200665
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (5 variants)
- not provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RXRB gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 5 | 5 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 2 |
Variants in RXRB
This is a list of pathogenic ClinVar variants found in the RXRB region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-33194833-G-GGGTGGA | Benign (Dec 31, 2019) | |||
| 6-33195026-C-T | Inborn genetic diseases | Uncertain significance (Oct 04, 2022) | ||
| 6-33195674-G-A | Benign (Sep 27, 2019) | |||
| 6-33196456-C-T | Inborn genetic diseases | Uncertain significance (May 23, 2023) | ||
| 6-33196472-C-T | Inborn genetic diseases | Likely benign (Mar 21, 2023) | ||
| 6-33196553-C-G | Inborn genetic diseases | Uncertain significance (Jun 13, 2022) | ||
| 6-33198386-C-T | Inborn genetic diseases | Uncertain significance (Dec 06, 2021) | ||
| 6-33199179-C-T | Inborn genetic diseases | Uncertain significance (Oct 04, 2022) | ||
| 6-33199227-G-A | Inborn genetic diseases | Uncertain significance (Sep 12, 2023) | ||
| 6-33199270-G-C | Inborn genetic diseases | Uncertain significance (Jun 01, 2023) | ||
| 6-33199270-G-T | Inborn genetic diseases | Uncertain significance (Feb 07, 2023) | ||
| 6-33199345-G-A | Inborn genetic diseases | Uncertain significance (Mar 31, 2023) | ||
| 6-33200287-C-G | Inborn genetic diseases | Uncertain significance (May 24, 2023) | ||
| 6-33200451-A-G | Inborn genetic diseases | Uncertain significance (Aug 01, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RXRB | protein_coding | protein_coding | ENST00000374685 | 10 | 7266 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00281 | 123951 | 0 | 5 | 123956 | 0.0000202 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.42 | 129 | 294 | 0.439 | 0.0000167 | 3394 |
| Missense in Polyphen | 42 | 145.88 | 0.28791 | 1531 | ||
| Synonymous | 2.51 | 78 | 112 | 0.698 | 0.00000568 | 1157 |
| Loss of Function | 4.11 | 1 | 21.7 | 0.0462 | 0.00000112 | 250 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000124 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000180 | 0.0000180 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE). {ECO:0000269|PubMed:1310259}.;
- Pathway
- Non-small cell lung cancer - Homo sapiens (human);Gastric cancer - Homo sapiens (human);Adipocytokine signaling pathway - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Thyroid hormone signaling pathway - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Thyroid cancer - Homo sapiens (human);NHR;Vitamin D Metabolism;Nuclear Receptors;PPAR signaling pathway;Vitamin A and Carotenoid Metabolism;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription;Signaling by Retinoic Acid;Signaling by Nuclear Receptors;a6b1 and a6b4 Integrin signaling;RXR and RAR heterodimerization with other nuclear receptor;Retinoic acid receptors-mediated signaling;Regulation of Androgen receptor activity
(Consensus)
Intolerance Scores
- loftool
- 0.140
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 44.54
Haploinsufficiency Scores
- pHI
- 0.322
- hipred
- Y
- hipred_score
- 0.785
- ghis
- 0.684
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rxrb
- Phenotype
- hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; normal 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); liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; immune system phenotype; vision/eye phenotype; 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); hearing/vestibular/ear phenotype; endocrine/exocrine gland phenotype; growth/size/body region 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); homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype;
Gene ontology
- Biological process
- transcription initiation from RNA polymerase II promoter;steroid hormone mediated signaling pathway;positive regulation of transcription by RNA polymerase II;retinoic acid receptor signaling pathway
- Cellular component
- nucleus;nucleoplasm
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;steroid hormone receptor activity;transcription coactivator activity;nuclear receptor activity;protein binding;zinc ion binding